KRIT1

gene
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Also known as CAM

Summary

KRIT1 (KRIT1 ankyrin repeat containing, HGNC:1573) is a protein-coding gene on chromosome 7q21.2, encoding Krev interaction trapped protein 1 (O00522). Component of the CCM signaling pathway which is a crucial regulator of heart and vessel formation and integrity.

This gene encodes a protein containing four ankyrin repeats, a band 4.1/ezrin/radixin/moesin (FERM) domain, and multiple NPXY sequences. The encoded protein is localized in the nucleus and cytoplasm. It binds to integrin cytoplasmic domain-associated protein-1 alpha (ICAP1alpha), and plays a critical role in beta1-integrin-mediated cell proliferation. It associates with junction proteins and RAS-related protein 1A (Rap1A), which requires the encoded protein for maintaining the integrity of endothelial junctions. It is also a microtubule-associated protein and may play a role in microtubule targeting. Mutations in this gene result in cerebral cavernous malformations. Multiple alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 889 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cerebral cavernous malformation 1 (Definitive, GenCC) — +1 more curated relationship
  • GWAS associations: 2
  • Clinical variants (ClinVar): 833 total — 279 pathogenic, 65 likely-pathogenic
  • Phenotypes (HPO): 33
  • MANE Select transcript: NM_194454

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1573
Approved symbolKRIT1
NameKRIT1 ankyrin repeat containing
Location7q21.2
Locus typegene with protein product
StatusApproved
AliasesCAM
Ensembl geneENSG00000001631
Ensembl biotypeprotein_coding
OMIM604214
Entrez889

Gene structure

Transcript identifiers

Ensembl transcripts: 81 — 33 protein_coding, 28 retained_intron, 17 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined

ENST00000340022, ENST00000394503, ENST00000394505, ENST00000394507, ENST00000412043, ENST00000413688, ENST00000422347, ENST00000425073, ENST00000425919, ENST00000430102, ENST00000433016, ENST00000440209, ENST00000444960, ENST00000445516, ENST00000452773, ENST00000454017, ENST00000458177, ENST00000466166, ENST00000470309, ENST00000475770, ENST00000486261, ENST00000487168, ENST00000489087, ENST00000684808, ENST00000685285, ENST00000685431, ENST00000686043, ENST00000686094, ENST00000686149, ENST00000686233, ENST00000686527, ENST00000686619, ENST00000686785, ENST00000687135, ENST00000687517, ENST00000687627, ENST00000687876, ENST00000688180, ENST00000688196, ENST00000688314, ENST00000688404, ENST00000688580, ENST00000688665, ENST00000688766, ENST00000688781, ENST00000689082, ENST00000689411, ENST00000689539, ENST00000689556, ENST00000689778, ENST00000689789, ENST00000690292, ENST00000690529, ENST00000690720, ENST00000690751, ENST00000690904, ENST00000690908, ENST00000691222, ENST00000691239, ENST00000691622, ENST00000691827, ENST00000691890, ENST00000692000, ENST00000692157, ENST00000692205, ENST00000692361, ENST00000692428, ENST00000692690, ENST00000692807, ENST00000693563, ENST00000905037, ENST00000905038, ENST00000905039, ENST00000905040, ENST00000905041, ENST00000905042, ENST00000936491, ENST00000967258, ENST00000967259, ENST00000967260, ENST00000967261

RefSeq mRNA: 34 — MANE Select: NM_194454 NM_001013406, NM_001350669, NM_001350670, NM_001350671, NM_001350672, NM_001350673, NM_001350674, NM_001350675, NM_001350676, NM_001350677, NM_001350678, NM_001350679, NM_001350680, NM_001350681, NM_001350682, NM_001350683, NM_001350684, NM_001350685, NM_001350686, NM_001350687, NM_001350688, NM_001350689, NM_001350690, NM_001350691, NM_001350692, NM_001350693, NM_001350694, NM_001350695, NM_001350696, NM_001350697, NM_004912, NM_194454, NM_194455, NM_194456

CCDS: CCDS34679, CCDS5624

Canonical transcript exons

ENST00000394505 — 19 exons

ExonStartEnd
ENSE000011700479223641392236542
ENSE000011700629224099392241152
ENSE000011700779224400292244149
ENSE000015186679224579092245914
ENSE000015186699224490292245171
ENSE000034685929221461192214777
ENSE000034738629223444992234592
ENSE000035011819220130792201423
ENSE000035272019223766792237759
ENSE000035326239223480892234923
ENSE000035514219221319592213401
ENSE000035676759221389292213979
ENSE000036114689222572092225827
ENSE000036313819222652692226682
ENSE000036319609222190292222053
ENSE000036569119219941392200804
ENSE000036946269222282292222978
ENSE000037881799223540392235646
ENSE000039269259224203492242137

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 95.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.1617 / max 311.1728, expressed in 1755 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
8478410.91221734
847830.5187258
847860.326292
847810.305063
847820.066516
847850.03335

Top tissues by expression

139 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370195.27gold quality
colonic epitheliumUBERON:000039795.02gold quality
corpus callosumUBERON:000233694.32gold quality
mucosa of stomachUBERON:000119993.39gold quality
endometriumUBERON:000129593.27gold quality
body of pancreasUBERON:000115092.56gold quality
tonsilUBERON:000237292.43gold quality
bone marrow cellCL:000209291.76gold quality
adrenal tissueUBERON:001830391.33gold quality
ventricular zoneUBERON:000305391.30gold quality
pancreasUBERON:000126490.99gold quality
uterine cervixUBERON:000000290.97gold quality
primary visual cortexUBERON:000243690.87gold quality
ovaryUBERON:000099290.78gold quality
right uterine tubeUBERON:000130290.75gold quality
pituitary glandUBERON:000000790.72gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047390.68gold quality
urinary bladderUBERON:000125590.66gold quality
thyroid glandUBERON:000204690.63gold quality
left ovaryUBERON:000211990.55gold quality
adenohypophysisUBERON:000219690.48gold quality
right lobe of thyroid glandUBERON:000111990.42gold quality
right ovaryUBERON:000211890.41gold quality
endocervixUBERON:000045890.38gold quality
left lobe of thyroid glandUBERON:000112090.32gold quality
cortex of kidneyUBERON:000122590.26gold quality
gall bladderUBERON:000211090.13gold quality
sural nerveUBERON:001548890.12gold quality
fundus of stomachUBERON:000116090.10gold quality
smooth muscle tissueUBERON:000113590.03gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

161 targeting KRIT1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-3646100.0073.565283
HSA-MIR-3163100.0077.238605
HSA-MIR-656-3P100.0072.152788
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-340-5P100.0072.504437
HSA-MIR-8485100.0077.574731
HSA-MIR-4533100.0069.482758
HSA-MIR-5692A100.0074.406850
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548N99.9871.944170
HSA-MIR-477599.9875.006394
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-365899.9673.874379
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-6778-3P99.9667.292693

Literature-anchored findings (GeneRIF, showing 40)

  • Experimentally determined additional 5’ UTR variants and additional mutations (in CCM1 study families) in coding exons that lead to frameshifts and premature truncations in the protein. (PMID:11161805)
  • Experimentally determined additional 5’ UTR alternatively spliced variants. Determined gene contains 20 exons. (PMID:11342228)
  • KRIT1/CCM1 mutation in a patient with retinal and cerebral cavernous angiomas. (PMID:11831930)
  • Integrin-binding protein also interacts with Krit 1 protein, cause of CCM1. (ICAP-1, integrin cytoplasmic domain-associated protein 1) (PMID:11854171)
  • In familial CCM1 samples, two new Krit1 mutations have been reported in four new upstream exons and six additional mutations have been discovered in the previously identified exons, demonstrating a mutation frequency of 47% in the 27 families studied. (PMID:11914398)
  • RNA analysis reveals that two point mutations actually activate cryptic splice-donor sites, causing aberrant splicing and leading to a frameshift and protein truncation (PMID:11941540)
  • Experimentally determined alternatively spliced variants in the 5’ coding region that alter the open reading frame and lead to premature translation termination codons. Determined that the 3’ UTR is larger than previously found. (PMID:12172908)
  • Krit1 mRNA expression in adult tissues (PMID:12204286)
  • Mutations in Krit1 are associated with familial cerebral cavernous malformations, but seldom a cause of sporadic cavernomas (PMID:12682320)
  • Identification of a novel KRIT1 mutation in an Italian family with cerebral cavernous malformation by the protein truncation test. (PMID:12810002)
  • We report a mutation causing a premature termination triplet in exon 17 of the Krit1 gene in a family with diagnoses of cerebral cavernous angioma (PMID:12877753)
  • KRIT1 is also present in cells and structures integral to the cerebral angiogenesis and formation of the blood-brain barrier, namely, endothelial cells and astrocytic foot processes, as well as pyramidal neurons in the cerebral cortex. (PMID:15046662)
  • The CCM1 gene was screened in 35 sporadic cases with either single or multiple CCM. It was found that 29% of the individuals with multiple CCM have a CCM1 mutation, whereas cases with only one malformation have none (PMID:15079030)
  • biallelic CCM1 somatic and germ line truncating mutation identification strongly supports the “two-hit” mechanism in this cerebral cavernous malformation lesion (PMID:15718512)
  • KRIT1, Malcavernin, and PDCD10 are differentially expressed in cerebral venous malformations and cerebral cavernous malformations (PMID:16239636)
  • CCM1 and CCM2 have similar expression patterns during development and are involved in the same pathway important for central nervous system vascular development (PMID:16373645)
  • Results confirm the conclusion that KRIT1 haploinsufficiency may be the underlying mechanism of cerebral cavernous malformations. (PMID:16529293)
  • SNX17 has a role in the indicated KRIT1 function in cell adhesion processes by integrin signaling (PMID:16712798)
  • Five percent of patients with familial cerebral cavernomas have retinal cavernomas. These lesions are clinically asymptomatic. They can be associated with any of the 3 cerebral cavernous malformation genes. (PMID:16769843)
  • Two new mutations in the KRIT1 gene in two Italian families affected by cerebral cavernous malformations. (PMID:17043900)
  • Mutations in CCM1/KRIT1 may be found in asymptomatic patients with retinal cavernous hemangioma. (PMID:17148043)
  • Krit1 interacts with malcavernin and may shuttle it through the nucleus via nuclear export signals, thereby regulating cellular function. (PMID:17290187)
  • we found a novel CCM1 gene mutation (Q66X) in a family with apparently asymptomatic old-aged mutation carriers and patients who either had skin angiomas alone or the full association of cerebral, spinal, and skin lesions (PMID:17440989)
  • Three novel and 2 described mutations were found in KRIT1. The families included 33 KRIT1 mutation carriers, 57.6% of whom had no symptoms. (PMID:17562932)
  • Rap1 increases KRIT-1 targeting to endothelial cell-cell junctions where it suppresses stress fibers and stabilizes junctional integrity. (PMID:17954608)
  • data are in agreement with a loss-of-function mechanism for CCM mutations, uncover an N-terminal CCM2 domain required for CCM1 binding, and demonstrate full-length CCM2 as the essential core protein in the CCM1/CCM2/CCM3 complex (PMID:18300272)
  • Krit1 and integrin cytoplasmic domain-associated protein-1 alpha (icap1alpha) act concordantly to play a critical role in beta 1-integrin-mediated cell proliferation. (PMID:18812969)
  • Biallelic germline and somatic mutations were identified in CCM1, CCM2 or PDCD10 from all forms of inherited cerebral cavernous malformations. (PMID:19088123)
  • Complete localized loss of either CCM1, CCM2 or CCM3 protein expression depend on the inherited mutation in cerebral cavernous malformations. (PMID:19088124)
  • Sequencing of KRIT1 identified a novel frameshift mutation in exon 15 (c.1561delC or p.Leu551X) which cosegregated with the phenotype observed in a family with cerebral cavernous malformations. (PMID:19092252)
  • mutations in the KRIT1 gene may cause phenotypically heterogeneous cutaneous vascular lesions other than those previously described as HCCVMs. (PMID:19182478)
  • The Multiplex Ligation-dependent Probe Amplification analysis revealed a new mutation, a heterozygous exon 9/10 deletion of Krit1, in the proband and in all affected family members. (PMID:19199464)
  • CCM1 is the most frequently mutated gene in cutaneous vascular malformations-familial cerebral cavernous malformations patients. (PMID:19453802)
  • C329X in KRIT1 is a founder mutation among CCM patients in Sardinia. (PMID:19454328)
  • Familial CCM1 cavernous malformations are unlikely to be associated with developmental venous anomalies, and sporadic malformations have a high rate of association with them (PMID:19833796)
  • We have identified a novel mutation in the KRIT1/CCM1 gene in a patient with both CCM and retinal cavernous hemangioma. (PMID:20306072)
  • The KRIT1-CCM2 interaction regulates endothelial junctional stability and vascular barrier function by suppressing activation of the RhoA/ROCK signaling pathway. This pathway is dysregulated in human cerebral cavernous malformation endothelium. (PMID:20308363)
  • Genetic variations could interfere with the proper CCM1/CCM2/CCM3 protein complex, thus explaining the observed clinical variability in cerebral cavernous malformations in a large family. (PMID:20419355)
  • Frame shift mutation in KRIT1 gene is associated with cerebral and multiple spinal cavernous malformations. (PMID:20689144)
  • We described the complete loss of 7q21.2 locus encompassing the KRIT1 gene and 4 flanking genes in a CCM family by using a dense set of 12 microsatellite markers. (PMID:20798775)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriokrit1ENSDARG00000098916
mus_musculusKrit1ENSMUSG00000000600
rattus_norvegicusKrit1ENSRNOG00000007937
caenorhabditis_eleganskri-1WBGENE00013955

Paralogs (1): FRMD8 (ENSG00000126391)

Protein

Protein identifiers

Krev interaction trapped protein 1O00522 (reviewed: O00522)

Alternative names: Cerebral cavernous malformations 1 protein

All UniProt accessions (20): A0A0C4DG23, A0A8I5KQD8, A0A8I5KQH3, A0A8I5KRK7, A0A8I5KUF9, A0A8I5KVW5, O00522, A0A8I5KVY1, A0A8I5KVY4, A0A8I5KW41, A0A8I5KWG2, A0A8I5KX77, A4D1F7, C9J718, C9JD43, C9JEW7, C9JF32, C9JIY2, C9JJM9, C9JXI9

UniProt curated annotations — full annotation on UniProt →

Function. Component of the CCM signaling pathway which is a crucial regulator of heart and vessel formation and integrity. Negative regulator of angiogenesis. Inhibits endothelial proliferation, apoptosis, migration, lumen formation and sprouting angiogenesis in primary endothelial cells. Promotes AKT phosphorylation in a NOTCH-dependent and independent manner, and inhibits ERK1/2 phosphorylation indirectly through activation of the DELTA-NOTCH cascade. Acts in concert with CDH5 to establish and maintain correct endothelial cell polarity and vascular lumen and these effects are mediated by recruitment and activation of the Par polarity complex and RAP1B. Required for the localization of phosphorylated PRKCZ, PARD3, TIAM1 and RAP1B to the cell junction, and cell junction stabilization. Plays a role in integrin signaling via its interaction with ITGB1BP1; this prevents the interaction between ITGB1 and ITGB1BP1. Microtubule-associated protein that binds to phosphatidylinositol 4,5-bisphosphate (PIP2)-containing membranes in a GTP-bound RAP1-dependent manner. Plays an important role in the maintenance of the intracellular reactive oxygen species (ROS) homeostasis to prevent oxidative cellular damage. Regulates the homeostasis of intracellular ROS through an antioxidant pathway involving FOXO1 and SOD2. Facilitates the down-regulation of cyclin-D1 (CCND1) levels required for cell transition from proliferative growth to quiescence by preventing the accumulation of intracellular ROS through the modulation of FOXO1 and SOD2 levels. May play a role in the regulation of macroautophagy through the down-regulation of the mTOR pathway.

Subunit / interactions. Interacts with CDH5. Found in a complex, at least composed of ITGB1BP1, KRIT1 and RAP1A. Interacts (via C-terminus FERM domain) with RAP1A (active GTP-bound form preferentially); the interaction does not induce the opening conformation of KRIT1. Interacts (via FERM domain) with RAP1B. Interacts (via N-terminus NPXY motif) with ITGB1BP1; the interaction induces the opening conformation of KRIT1 and competes with ITGB1 for ITGB1BP1 interaction. Interacts with HEG1 and CCM2; greatly facilitates CCM2-binding to HEG1. Associates (via N-terminus and C-terminus regions) with microtubules; the interaction is inhibited in presence of ITGB1BP1 and active GTP-bound RAP1A.

Subcellular location. Cytoplasm. Cytoskeleton. Cell membrane. Cell junction.

Tissue specificity. Low levels in brain. Very weak expression found in heart and muscle.

Disease relevance. Cerebral cavernous malformations 1 (CCM1) [MIM:116860] A form of cerebral cavernous malformations, a congenital vascular anomaly of the central nervous system that can result in hemorrhagic stroke, seizures, recurrent headaches, and focal neurologic deficits. The lesions are characterized by grossly enlarged blood vessels consisting of a single layer of endothelium and without any intervening neural tissue, ranging in diameter from a few millimeters to several centimeters. CCM1 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The FERM domain mediates binding to RAP1A and RAP1B and is necessary for binding to phosphatidylinositol 4,5-bisphosphate (PIP2). The N-terminal domain has structural similarity to the nudix hydrolase domain, despite the absence of a nudix box and low sequence similarity with nudix hydrolase domains. The N-terminus and the C-terminus part associate together via the NPAY binding motif and adopt a lose conformation that is disrupted by ITGB1BP1, but not by RAP1A. Contains 4 ANK repeats that precede the FERM domain.

Isoforms (3)

UniProt IDNamesCanonical?
O00522-11yes
O00522-22
O00522-33

RefSeq proteins (34): NP_001013424, NP_001337598, NP_001337599, NP_001337600, NP_001337601, NP_001337602, NP_001337603, NP_001337604, NP_001337605, NP_001337606, NP_001337607, NP_001337608, NP_001337609, NP_001337610, NP_001337611, NP_001337612, NP_001337613, NP_001337614, NP_001337615, NP_001337616, NP_001337617, NP_001337618, NP_001337619, NP_001337620, NP_001337621, NP_001337622, NP_001337623, NP_001337624, NP_001337625, NP_001337626, NP_004903, NP_919436, NP_919437, NP_919438 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000299FERM_domainDomain
IPR002110Ankyrin_rptRepeat
IPR011993PH-like_dom_sfHomologous_superfamily
IPR014352FERM/acyl-CoA-bd_prot_sfHomologous_superfamily
IPR019748FERM_centralDomain
IPR019749Band_41_domainDomain
IPR032022NUDIXDomain
IPR035963FERM_2Homologous_superfamily
IPR036770Ankyrin_rpt-contain_sfHomologous_superfamily
IPR041791KRIT1_FERM_CDomain
IPR043058NUDIX_sfHomologous_superfamily
IPR051594KRIT1/FRMD8Family
IPR056485ARM_KRIT1Domain
IPR057096KRIT1_FRMD8_FERM_CDomain

Pfam: PF00373, PF16705, PF24521, PF24522

UniProt features (90 total): helix 31, strand 22, mutagenesis site 14, turn 7, repeat 4, sequence conflict 3, region of interest 3, splice variant 2, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

15 structures.

PDBMethodResolution (Å)
4HDOX-RAY DIFFRACTION1.67
4JIFX-RAY DIFFRACTION1.7
6OQ4X-RAY DIFFRACTION1.75
6OQ3X-RAY DIFFRACTION1.85
6UZKX-RAY DIFFRACTION1.92
4DXAX-RAY DIFFRACTION1.95
4HDQX-RAY DIFFRACTION1.95
8SU8X-RAY DIFFRACTION2.01
8T09X-RAY DIFFRACTION2.15
8T7VX-RAY DIFFRACTION2.25
3U7DX-RAY DIFFRACTION2.49
4DX8X-RAY DIFFRACTION2.54
5D68X-RAY DIFFRACTION2.91
4TKNX-RAY DIFFRACTION3
9PVGX-RAY DIFFRACTION3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00522-F183.010.57

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (14):

PositionPhenotype
47–50reduces interaction with microtubules, but not with itgb1bp1.
176strongly reduces itgb1bp1 binding; when associated with d-182.
179strongly reduces itgb1bp1 binding; when associated with a-179.
182strongly reduces itgb1bp1 binding; when associated with d-176.
185strongly reduces itgb1bp1 binding; when associated with a-179.
192–195reduces interaction with itgb1bp1.
192reduces itgb1bp1 binding; when associated with a-195.
195reduces itgb1bp1 binding; when associated with a-192.
430impairs interaction with rap1b.
432impairs interaction with rap1b.
45240-fold-reduced affinity for rap1a.
452impairs interaction with rap1b.
717strongly reduced affinity for heg1; when associated with a-721.
721strongly reduced affinity for heg1; when associated with a-717.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 298 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_CELL_PROLIFERATION, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_EPITHELIUM_DEVELOPMENT, WANG_CLIM2_TARGETS_UP, GGTGTGT_MIR329, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, TGACCTY_ERR1_Q2, MORF_HDAC2, GGGTGGRR_PAX4_03, MORF_TERF1, GOBP_ESTABLISHMENT_OF_CELL_POLARITY, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_CELL_REDOX_HOMEOSTASIS, GOBP_REGULATION_OF_ENDOTHELIAL_CELL_MIGRATION

GO Biological Process (13): angiogenesis (GO:0001525), negative regulation of endothelial cell proliferation (GO:0001937), endothelium development (GO:0003158), small GTPase-mediated signal transduction (GO:0007264), negative regulation of endothelial cell migration (GO:0010596), negative regulation of angiogenesis (GO:0016525), integrin activation (GO:0033622), cell redox homeostasis (GO:0045454), regulation of angiogenesis (GO:0045765), regulation of establishment of cell polarity (GO:2000114), negative regulation of endothelial cell apoptotic process (GO:2000352), negative regulation of developmental process (GO:0051093), regulation of multicellular organismal development (GO:2000026)

GO Molecular Function (4): phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), microtubule binding (GO:0008017), GTPase regulator activity (GO:0030695), protein binding (GO:0005515)

GO Cellular Component (8): obsolete extracellular space (GO:0005615), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cell-cell junction (GO:0005911), protein-containing complex (GO:0032991), membrane (GO:0016020), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
angiogenesis2
regulation of developmental process2
cellular anatomical structure2
blood vessel morphogenesis1
anatomical structure formation involved in morphogenesis1
endothelial cell proliferation1
regulation of endothelial cell proliferation1
negative regulation of epithelial cell proliferation1
epithelium development1
intracellular signaling cassette1
regulation of endothelial cell migration1
negative regulation of cell migration1
endothelial cell migration1
regulation of angiogenesis1
negative regulation of blood vessel morphogenesis1
protein-containing complex assembly1
cellular homeostasis1
regulation of anatomical structure morphogenesis1
regulation of vasculature development1
establishment of cell polarity1
regulation of establishment or maintenance of cell polarity1
negative regulation of apoptotic process1
endothelial cell apoptotic process1
regulation of endothelial cell apoptotic process1
developmental process1
negative regulation of biological process1
multicellular organism development1
regulation of multicellular organismal process1
phosphatidylinositol phosphate binding1
phosphatidylinositol bisphosphate binding1
tubulin binding1
GTPase activity1
nucleoside-triphosphatase regulator activity1
binding1
intracellular anatomical structure1
intracellular membraneless organelle1
membrane1
cell periphery1
anchoring junction1
cellular_component1

Protein interactions and networks

STRING

1182 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KRIT1CCM2Q9BSQ5998
KRIT1RAP1AP10113996
KRIT1PDCD10Q9BUL8996
KRIT1ITGB1BP1O14713992
KRIT1SNX17Q15036967
KRIT1HEG1Q9ULI3966
KRIT1STK25O00506847
KRIT1MAP3K3Q99759821
KRIT1CDH5P33151773
KRIT1RAP1BP09526768
KRIT1RASIP1Q5U651754
KRIT1RAP2AP10114727
KRIT1RHOAP06749709
KRIT1ACVRL1P37023706
KRIT1MYL2P10916700

IntAct

45 interactions, top by confidence:

ABTypeScore
CCM2KRIT1psi-mi:“MI:0915”(physical association)0.960
KRIT1CCM2psi-mi:“MI:0915”(physical association)0.960
KRIT1CCM2psi-mi:“MI:0914”(association)0.960
KRIT1CCM2psi-mi:“MI:0407”(direct interaction)0.960
CCM2KRIT1psi-mi:“MI:0914”(association)0.960
ITGB1BP1KRIT1psi-mi:“MI:0915”(physical association)0.740
KRIT1ITGB1BP1psi-mi:“MI:0915”(physical association)0.740
HEG1KRIT1psi-mi:“MI:0915”(physical association)0.730
HEG1KRIT1psi-mi:“MI:0407”(direct interaction)0.730
KRIT1UBE2Kpsi-mi:“MI:0915”(physical association)0.560
TLNRD1KRIT1psi-mi:“MI:0914”(association)0.530
CCM2KRIT1psi-mi:“MI:0914”(association)0.500

BioGRID (63): KRIT1 (Affinity Capture-RNA), RAP1A (Two-hybrid), KRIT1 (Two-hybrid), KRIT1 (Two-hybrid), CCM2 (Two-hybrid), ITGB1BP1 (Two-hybrid), KRIT1 (Affinity Capture-MS), ITGB1BP1 (Affinity Capture-MS), HEG1 (Affinity Capture-MS), SLC34A2 (Affinity Capture-MS), UBFD1 (Affinity Capture-MS), KRIT1 (Synthetic Lethality), UBE2K (Two-hybrid), ITGB1BP1 (Two-hybrid), ITGB1BP1 (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GW35, A6QNM3, B0R034, B1ANS9, B9EK06, D2KC46, D3ZY60, F1MS15, F1P065, F1REV3, O00522, O15091, O75747, P10911, P58069, Q008S8, Q14449, Q14D04, Q15283, Q32NR9, Q45GW3, Q4R366, Q4R6T7, Q5H9U9, Q5K651, Q5PQS3, Q5XGX5, Q5XIZ9, Q5ZLD2, Q60862, Q63713, Q69Z37, Q6DCF6, Q6S5J6, Q6TNJ1, Q75PQ8, Q80W71, Q86VD1, Q86YR7, Q8C5W4

Diamond homologs: F1REV3, O00522, Q10728, Q6S5J6, Q6TNJ1, Q9DBR7, A2AQH4, A4II29, B2RR83, G3I6Z6, O13987, O14974, O60237, P46531, P83757, Q01705, Q02979, Q03017, Q07008, Q0VC93, Q18297, Q1RJ94, Q28FJ2, Q337A0, Q3SX00, Q3UES3, Q3UMT1, Q3V096, Q4FE45, Q4JHE0, Q5H9F3, Q5I1X5, Q5R746, Q5R8C8, Q5U5A6, Q61982, Q6DRG7, Q6KAE5, Q7T3X9, Q7T3Y0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

833 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic279
Likely pathogenic65
Uncertain significance265
Likely benign102
Benign22

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1068679NM_194454.3(KRIT1):c.1333C>T (p.Gln445Ter)Pathogenic
1068705NM_194454.3(KRIT1):c.1616T>G (p.Leu539Ter)Pathogenic
1069273NM_194454.3(KRIT1):c.1297del (p.Ser433fs)Pathogenic
1070438NM_194454.3(KRIT1):c.1446dup (p.His483fs)Pathogenic
1070522NM_194454.3(KRIT1):c.206T>A (p.Leu69Ter)Pathogenic
1071790NM_194454.3(KRIT1):c.1099dup (p.His367fs)Pathogenic
1071796NM_194454.3(KRIT1):c.382G>T (p.Gly128Ter)Pathogenic
1072402NC_000007.13:g.(?91829918)(91851387_?)delPathogenic
1072403NC_000007.13:g.(?91863743)(91871469_?)delPathogenic
1073009NM_194454.3(KRIT1):c.1162C>T (p.Gln388Ter)Pathogenic
1074210NM_194454.3(KRIT1):c.250C>T (p.Gln84Ter)Pathogenic
1074229NM_194454.3(KRIT1):c.2113A>T (p.Lys705Ter)Pathogenic
1074264NC_000007.13:g.(?91851196)(91871469_?)delPathogenic
1074265NC_000007.13:g.(?91866961)(91871469_?)delPathogenic
1074639NM_194454.3(KRIT1):c.2049T>G (p.Tyr683Ter)Pathogenic
1074766NM_194454.3(KRIT1):c.1389_1390del (p.Ile463fs)Pathogenic
1075474NM_194454.3(KRIT1):c.1980_1981delinsGT (p.Gly661Ter)Pathogenic
1075800NM_194454.3(KRIT1):c.1212G>A (p.Trp404Ter)Pathogenic
1187060NM_194454.3(KRIT1):c.1146+1G>TPathogenic
1252052NM_194454.3(KRIT1):c.992A>G (p.Tyr331Cys)Pathogenic
1254168NM_194454.3(KRIT1):c.699del (p.Leu233fs)Pathogenic
1284973NM_194454.3(KRIT1):c.1166del (p.Gly389fs)Pathogenic
1285155NM_194454.3(KRIT1):c.1412-1G>CPathogenic
1285206NM_194454.3(KRIT1):c.1287del (p.Ser430fs)Pathogenic
1299386NM_194454.3(KRIT1):c.1664C>T (p.Ala555Val)Pathogenic
1320113NM_194454.3(KRIT1):c.1444C>T (p.Gln482Ter)Pathogenic
1331022NM_194454.3(KRIT1):c.1287dup (p.Ser430fs)Pathogenic
1333479NM_194454.3(KRIT1):c.1097del (p.Gly366fs)Pathogenic
1355783NC_000007.14:g.92201424dupPathogenic
1358522NM_194454.3(KRIT1):c.2100_2101dup (p.Ser701fs)Pathogenic

SpliceAI

3108 predictions. Top by Δscore:

VariantEffectΔscore
7:92213886:GCTTA:Gdonor_loss1.0000
7:92213887:CTTA:Cdonor_loss1.0000
7:92213888:TTA:Tdonor_loss1.0000
7:92213889:TAC:Tdonor_loss1.0000
7:92213975:CTTCA:Cacceptor_gain1.0000
7:92213978:CA:Cacceptor_gain1.0000
7:92213980:C:CCacceptor_gain1.0000
7:92214609:A:ACdonor_gain1.0000
7:92214610:C:CAdonor_gain1.0000
7:92214779:T:Cacceptor_gain1.0000
7:92221915:T:TAdonor_gain1.0000
7:92221931:CATCT:Cdonor_gain1.0000
7:92222689:T:Cacceptor_gain1.0000
7:92222691:A:Cacceptor_gain1.0000
7:92222693:A:Cacceptor_gain1.0000
7:92222820:A:ACdonor_gain1.0000
7:92222821:C:CCdonor_gain1.0000
7:92222821:CTGA:Cdonor_gain1.0000
7:92222821:CTGAG:Cdonor_gain1.0000
7:92222975:CATA:Cacceptor_gain1.0000
7:92222977:TA:Tacceptor_gain1.0000
7:92222979:C:CCacceptor_gain1.0000
7:92225714:TCTTA:Tdonor_loss1.0000
7:92225715:CTTA:Cdonor_loss1.0000
7:92225716:TTA:Tdonor_loss1.0000
7:92225717:TACTG:Tdonor_loss1.0000
7:92225718:A:ACdonor_gain1.0000
7:92225718:ACTGG:Adonor_loss1.0000
7:92225719:C:Adonor_loss1.0000
7:92225719:C:CTdonor_gain1.0000

AlphaMissense

4868 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:92234903:A:CN250K1.000
7:92234903:A:TN250K1.000
7:92237684:A:TV113D1.000
7:92242089:C:GR16P1.000
7:92213214:A:GL669P0.999
7:92213346:A:GF625S0.999
7:92221935:T:AR510S0.999
7:92221935:T:GR510S0.999
7:92221936:C:AR510I0.999
7:92222006:A:GW487R0.999
7:92222006:A:TW487R0.999
7:92222044:A:GL474P0.999
7:92222843:A:GW464R0.999
7:92222843:A:TW464R0.999
7:92222845:A:TI463K0.999
7:92222951:C:GD428H0.999
7:92222962:A:TI424K0.999
7:92226551:A:GL374P0.999
7:92226584:G:TA363D0.999
7:92226587:G:TA362D0.999
7:92226599:G:TP358H0.999
7:92226616:A:CN352K0.999
7:92226616:A:TN352K0.999
7:92234451:G:CC329W0.999
7:92234452:C:TC329Y0.999
7:92234453:A:GC329R0.999
7:92234467:G:CP324R0.999
7:92234467:G:TP324H0.999
7:92234474:A:GW322R0.999
7:92234474:A:TW322R0.999

dbSNP variants (sampled 300 via entrez): RS1000131072 (7:92221064 C>T), RS1000153086 (7:92236254 G>C), RS1000242654 (7:92221478 T>C), RS1000300337 (7:92199006 T>C,G), RS1000384813 (7:92233763 C>A), RS1000449073 (7:92227981 C>A,T), RS1000505571 (7:92236642 A>G), RS1000513814 (7:92243940 T>A,C), RS1000539467 (7:92215068 G>A), RS1000602788 (7:92233595 C>T), RS1000635953 (7:92228253 G>A,C), RS1000648626 (7:92246102 G>C), RS1000756633 (7:92203777 C>G,T), RS1000786709 (7:92202789 T>C), RS1000843107 (7:92209609 T>C)

Disease associations

OMIM: gene MIM:604214 | disease phenotypes: MIM:116860, MIM:600419

GenCC curated gene-disease

DiseaseClassificationInheritance
cerebral cavernous malformation 1DefinitiveAutosomal dominant
famililal cerebral cavernous malformationsSupportiveAutosomal dominant

Mondo (6): cerebral cavernous malformation (MONDO:0000820), cerebral cavernous malformation 1 (MONDO:0020724), angiokeratoma corporis diffusum with arteriovenous fistulas (MONDO:0010885), famililal cerebral cavernous malformations (MONDO:0031037), cavernous hemangioma (MONDO:0003155), vascular dementia (MONDO:0004648)

Orphanet (2): Familial cerebral cavernous malformation (Orphanet:221061), NON RARE IN EUROPE: Cerebral cavernous malformations (Orphanet:164)

HPO phenotypes

33 total (30 of 33 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000951Abnormality of the skin
HP:0001028Hemangioma
HP:0001048Cavernous hemangioma
HP:0001250Seizure
HP:0001324Muscle weakness
HP:0001342Cerebral hemorrhage
HP:0002170Intracranial hemorrhage
HP:0002315Headache
HP:0002514Cerebral calcification
HP:0002516Increased intracranial pressure
HP:0002572Episodic vomiting
HP:0002650Scoliosis
HP:0002858Meningioma
HP:0003011Abnormality of the musculature
HP:0003401Paresthesia
HP:0003829Typified by incomplete penetrance
HP:0006576Hepatic vascular malformations
HP:0007797Developmental retinal vascular malformation
HP:0007872Choroidal hemangioma
HP:0009588Vestibular schwannoma
HP:0009592Astrocytoma
HP:0010512Adrenal calcification
HP:0011276Vascular skin abnormality
HP:0011513Retinal cavernous hemangioma
HP:0012721Venous malformation
HP:0012748Focal T2 hyperintense brainstem lesion
HP:0012749Focal T2 hypointense brainstem lesion
HP:0030430Neuroma
HP:0033522Cerebral cavernous malformation

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006993_10Hippocampal volume in Alzheimer’s disease dementia2.000000e-07
GCST008526_36Coffee consumption1.000000e-07

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005035hippocampal volume
EFO:0006781coffee consumption measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D015140Dementia, VascularC10.228.140.300.400; C10.228.140.300.510.800.500; C10.228.140.380.230; C10.228.140.695.500; C14.907.137.126.372.500; C14.907.253.560.350.500; F03.615.400.350
D006392Hemangioma, CavernousC04.557.645.375.385; C10.228.140.232.625; C14.907.454.385; C15.378.463.515.385
C563940Angiokeratoma Corporis Diffusum with Arteriovenous Fistulas (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, increases abundance, increases expression, decreases expression3
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
bisphenol Aincreases expression1
beta-lapachonedecreases expression, increases expression1
sodium arsenitedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
pentanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608increases reaction, affects binding1
K 7174increases expression1
jinfukangdecreases expression1
Bortezomibincreases expression1
Irinotecandecreases expression1
Resveratrolaffects cotreatment, increases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1
Atrazinedecreases expression1
Coaldecreases expression, increases abundance1
Cocaineincreases expression1
Diethylhexyl Phthalatedecreases expression1
Folic Aciddecreases expression1

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C1V1NFHHMUi001-AInduced pluripotent stem cellMale

Clinical trials (associated diseases)

108 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00165763PHASE4COMPLETEDEfficacy and Safety of Donepezil Hydrochloride (Aricept) in Vascular Dementia
NCT00847860PHASE4COMPLETEDCilostazol Verse Asprin for Vascular Dementia in Poststroke Patients With White Matter Lesions
NCT00947531PHASE4COMPLETEDA Clinical Trial to Evaluate the Safety and Efficacy of 20 ml Cerebrolysin in Patients With Vascular Dementia
NCT00950430PHASE4ENROLLING_BY_INVITATIONImaging of Brain Amyloid Plaques in the Aging Population
NCT00099216PHASE3COMPLETEDEfficacy and Safety of Rivastigmine Capsules in Patients With Probable Vascular Dementia
NCT00130338PHASE3COMPLETEDRivastigmine Capsules in Patients With Probable Vascular Dementia
NCT00209456PHASE3COMPLETEDDopamine Transporter Scintigraphy Imaging (DAT-Imaging) in Patients With Lewy Body Dementia
NCT00249158PHASE3COMPLETEDA Study of the Effectiveness and Safety of Risperidone in the Treatment of Behavioral Disturbances in Patients With Dementia
NCT00261573PHASE3COMPLETEDA Study of the Safety and Effectiveness of Galantamine Versus Placebo in the Treatment of Patients With Vascular Dementia or Mixed Dementia
NCT00621647PHASE3COMPLETEDSeroquel- Agitation Associated With Dementia
NCT02453932PHASE3COMPLETEDEfficacy and Safety of Tianzhi Granule in Mild to Moderate Vascular Dementia
NCT03682185PHASE3COMPLETEDThe Healthy Patterns Sleep Study
NCT03789760PHASE3COMPLETEDThe Clinical Trial of Chinese Herbal Medicine (SaiLuoTong) Capsule
NCT03804229PHASE3ACTIVE_NOT_RECRUITINGEfficacy and Safety of Butylphthalide Soft Capsule for the Treatment of Vascular Dementia
NCT03986424PHASE3COMPLETEDLocal Study of Akatinol Memantine in VaD in Russia
NCT04552041PHASE3COMPLETEDProspekta in the Treatment of Cognitive, Behavioral and Psychiatric Disorders in Patients With Vascular Dementia.
NCT03474614PHASE2TERMINATEDEffect of Oral Propranolol on mRNA Expresssion in Symptomatic Cavernous Malformation
NCT03589014PHASE2COMPLETEDTreat_CCM: Propranolol in Familial Cerebral Cavernous Malformation
NCT05085561PHASE2COMPLETEDThe Symptomatic Cerebral Cavernous Malformation Trial of REC-994
NCT01466543PHASE2UNKNOWNEffect of Zydena (Udenafil) on Cerebral Blood Flow and Peripheral Blood Viscosity
NCT01475578PHASE2COMPLETEDStudy of STA-1 Capsule in Patients With Vascular Dementia (Marrow-Sea Deficiency)
NCT01608217PHASE2COMPLETEDDelta-THC in Dementia
NCT01761227PHASE2COMPLETEDEfficacy and Safety of Fufangdanshen Tablets in Mild to Moderate Vascular Dementia
NCT01953705PHASE2UNKNOWNn-3 PUFA for Vascular Cognitive Aging
NCT01965756PHASE2COMPLETEDEffect of Insulin Sensitizer Metformin on AD Biomarkers
NCT01978730PHASE2UNKNOWNThe Clinical Trial of Chinese Herbal Medicine SaiLuoTong Capsule
NCT02467413PHASE2WITHDRAWNBAC in Patient With Alzheimer’s Disease or Vascular Dementia
NCT03230071PHASE2COMPLETEDEfficacy and Safety of TMBCZG in Mild to Moderate Vascular Dementia
NCT04109963PHASE2UNKNOWNTrial of Remote Ischemic Pre-conditioning in Vascular Cognitive Impairment
NCT05371639PHASE2UNKNOWNEfficacy and Safety of Tian Ma Bian Chun Zhi Gan Tablets in Mild to Moderate Vascular Dementia
NCT00783523PHASE1COMPLETEDInfluence of MMP on Brain AVM Hemorrhage
NCT00457769PHASE1UNKNOWNAricept to Improve Functional Tasks in Vascular Dementia
NCT03702543PHASE1UNKNOWNManaging Vascular Dementia Risk Factors With SymTrend
NCT04567745PHASE1COMPLETEDAutomated Retinal Image Analysis System (EyeQuant) for Computation of Vascular Biomarkers
NCT01764451EARLY_PHASE1TERMINATEDPermeability MRI in Cerebral Cavernous Malformations Type 1 in New Mexico: Effects of Statins
NCT01764529Not specifiedACTIVE_NOT_RECRUITINGModifiers of Disease Severity in Cerebral Cavernous Malformations
NCT03467295Not specifiedUNKNOWNTreatments and Outcomes of Untreated Cerebral Cavernous Malformations in CHina.
NCT03652181Not specifiedCOMPLETEDCASH (Cavernous Angiomas With Symptomatic Hemorrhage) Trial Readiness
NCT06983132Not specifiedRECRUITINGNatural History of Familial Cerebral Cavernous Malformations: the CCM_Italia Cohort Study
NCT02603328PHASE1/PHASE2COMPLETEDAtorvastatin Treatment of Cavernous Angiomas With Symptomatic Hemorrhage Exploratory Proof of Concept (AT CASH EPOC) Trial