CRIP3
gene geneOn this page
Also known as TLP-AbA480N24.2TLP
Summary
CRIP3 (cysteine rich protein 3, HGNC:17751) is a protein-coding gene on chromosome 6p21.1, encoding Cysteine-rich protein 3 (Q6Q6R5).
Predicted to enable metal ion binding activity. Predicted to act upstream of or within T cell proliferation. Predicted to be located in cytoplasm.
Source: NCBI Gene 401262 — automated summary from GO annotations (Alliance of Genome Resources).
At a glance
- GWAS associations: 20
- Clinical variants (ClinVar): 37 total
- GTEx eGene: eQTL in 13 tissues, sQTL in 2 (q < 0.05)
- Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.04 (unconstrained)
- MANE Select transcript:
NM_206922
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:17751 |
| Approved symbol | CRIP3 |
| Name | cysteine rich protein 3 |
| Location | 6p21.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | TLP-A, bA480N24.2, TLP |
| Ensembl gene | ENSG00000146215 |
| Ensembl biotype | protein_coding |
| Entrez | 401262 |
Gene structure
Transcript identifiers
Ensembl transcripts: 34 — 24 protein_coding, 7 nonsense_mediated_decay, 3 retained_intron
MANE Select: ENST00000372569
Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 2, TSL 3: 3
ENST00000372569, ENST00000274990, ENST00000416431, ENST00000451294, ENST00000477866, ENST00000485819, ENST00000487744, ENST00000875330, ENST00000875331, ENST00000875332, ENST00000875333, ENST00000917954, ENST00000917955, ENST00000917956, ENST00000917957, ENST00000917958, ENST00000917959, ENST00000917960, ENST00000917961, ENST00000917962, ENST00000917963, ENST00000996765, ENST00000996766, ENST00001027280, ENST00001027281, ENST00001077667, ENST00001077668, ENST00001077669, ENST00001077670, ENST00001077672, ENST00001077673, ENST00001077674, ENST00001077676, ENST00001140165
RefSeq mRNA: 2 — MANE Select: NM_206922
NM_001366068, NM_206922
CCDS: CCDS4894
Canonical transcript exons
ENST00000372569 — 8 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000974499 | 43308315 | 43308409 |
| ENSE00000974501 | 43307612 | 43307743 |
| ENSE00000974502 | 43306446 | 43306517 |
| ENSE00000974503 | 43306219 | 43306313 |
| ENSE00001458118 | 43305472 | 43305875 |
| ENSE00003545360 | 43307839 | 43307896 |
| ENSE00003570712 | 43306067 | 43306124 |
| ENSE00003902020 | 43308750 | 43308826 |
Expression profiles
Bgee: expression breadth ubiquitous, 165 present calls, max score 95.03.
FANTOM5 (CAGE): breadth broad, TPM avg 1.1956 / max 53.0668, expressed in 275 samples.
Highest expression (Bgee): apex of heart, testis, cerebellar hemisphere, hemisphere of cerebellum, cerebellar cortex.
Genetic regulation across tissues (GTEx eQTL / sQTL)
CRIP3 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 13 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.
15 significant tissue × QTL associations:
| Tissue | QTL | q-value | Slope | Lead variant |
|---|---|---|---|---|
| Heart Left Ventricle | eqtl | 5.9e-14 | -0.32 | 6:43305866:A:G |
| Testis | sqtl | 3.8e-10 | -0.53 | 6:43305866:A:G |
| Liver | eqtl | 3.1e-09 | -0.39 | 6:43301291:A:C |
| Heart Atrial Appendage | eqtl | 2.0e-07 | +0.28 | 6:43292274:A:C |
| Testis | eqtl | 1.8e-04 | -0.11 | 6:43292274:A:C |
| Skin Sun Exposed Lower leg | eqtl | 4.8e-03 | -0.15 | 6:43336269:C:A |
| Cells EBV-transformed lymphocytes | sqtl | 1.0e-02 | -0.42 | 6:43396756:G:A |
| Brain Anterior cingulate cortex BA24 | eqtl | 1.0e-02 | -1.77 | 6:43025564:A:G |
| Artery Tibial | eqtl | 1.4e-02 | -0.32 | 6:43168060:G:A |
| Skin Not Sun Exposed Suprapubic | eqtl | 2.7e-02 | -0.31 | 6:43465542:G:A |
| Brain Hippocampus | eqtl | 2.7e-02 | -2.64 | 6:43025564:A:G |
| Brain Spinal cord cervical c-1 | eqtl | 3.9e-02 | -2.28 | 6:43239300:T:C |
| Muscle Skeletal | eqtl | 4.4e-02 | -0.35 | 6:43785985:G:A |
| Adipose Subcutaneous | eqtl | 4.5e-02 | -0.46 | 6:42623491:G:A |
| Ovary | eqtl | 5.0e-02 | -0.97 | 6:43884123:G:A |
FANTOM5 promoters
2 alternative TSS:
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 73675 | 1.0381 | 246 |
| 73676 | 0.1574 | 90 |
Top tissues by expression
showing 100 of 241 tissues by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| apex of heart | UBERON:0002098 | 95.03 | gold quality |
| right testis | UBERON:0004534 | 92.37 | gold quality |
| left testis | UBERON:0004533 | 92.14 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 90.09 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 90.00 | gold quality |
| cerebellar cortex | UBERON:0002129 | 89.98 | gold quality |
| testis | UBERON:0000473 | 88.30 | gold quality |
| cerebellum | UBERON:0002037 | 88.29 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 87.70 | gold quality |
| right lobe of liver | UBERON:0001114 | 85.23 | gold quality |
| granulocyte | CL:0000094 | 85.16 | gold quality |
| heart left ventricle | UBERON:0002084 | 84.88 | gold quality |
| cardiac ventricle | UBERON:0002082 | 84.43 | gold quality |
| nucleus accumbens | UBERON:0001882 | 83.88 | gold quality |
| right frontal lobe | UBERON:0002810 | 81.96 | gold quality |
| putamen | UBERON:0001874 | 81.85 | gold quality |
| caudate nucleus | UBERON:0001873 | 81.47 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 81.34 | gold quality |
| amygdala | UBERON:0001876 | 81.14 | gold quality |
| spleen | UBERON:0002106 | 80.55 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 79.51 | gold quality |
| hypothalamus | UBERON:0001898 | 79.40 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 77.06 | gold quality |
| lymph node | UBERON:0000029 | 77.05 | gold quality |
| heart | UBERON:0000948 | 76.87 | gold quality |
| sperm | CL:0000019 | 76.36 | silver quality |
| cortical plate | UBERON:0005343 | 76.34 | gold quality |
| brain | UBERON:0000955 | 76.09 | gold quality |
| liver | UBERON:0002107 | 75.49 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 75.18 | gold quality |
| forebrain | UBERON:0001890 | 74.96 | gold quality |
| vena cava | UBERON:0004087 | 74.54 | gold quality |
| monocyte | CL:0000576 | 74.27 | gold quality |
| spinal cord | UBERON:0002240 | 74.25 | gold quality |
| leukocyte | CL:0000738 | 74.22 | gold quality |
| neocortex | UBERON:0001950 | 74.22 | gold quality |
| substantia nigra | UBERON:0002038 | 73.60 | gold quality |
| cerebral cortex | UBERON:0000956 | 73.39 | gold quality |
| Ammon’s horn | UBERON:0001954 | 73.26 | gold quality |
| frontal cortex | UBERON:0001870 | 73.11 | gold quality |
| adult mammalian kidney | UBERON:0000082 | 73.07 | gold quality |
| kidney epithelium | UBERON:0004819 | 72.93 | gold quality |
| upper arm skin | UBERON:0004263 | 72.83 | gold quality |
| midbrain | UBERON:0001891 | 72.66 | gold quality |
| cortex of kidney | UBERON:0001225 | 72.48 | gold quality |
| prostate gland | UBERON:0002367 | 72.40 | gold quality |
| right atrium auricular region | UBERON:0006631 | 72.23 | gold quality |
| prefrontal cortex | UBERON:0000451 | 72.15 | gold quality |
| temporal lobe | UBERON:0001871 | 71.98 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 71.98 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 71.82 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 71.77 | gold quality |
| cardiac atrium | UBERON:0002081 | 71.36 | gold quality |
| ventricular zone | UBERON:0003053 | 71.34 | gold quality |
| right ovary | UBERON:0002118 | 71.12 | gold quality |
| blood | UBERON:0000178 | 70.68 | gold quality |
| vermiform appendix | UBERON:0001154 | 70.62 | gold quality |
| small intestine | UBERON:0002108 | 70.57 | gold quality |
| pancreatic ductal cell | CL:0002079 | 70.41 | silver quality |
| primary visual cortex | UBERON:0002436 | 70.35 | gold quality |
| endocervix | UBERON:0000458 | 70.05 | gold quality |
| tibial nerve | UBERON:0001323 | 69.94 | gold quality |
| ganglionic eminence | UBERON:0004023 | 69.92 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 69.49 | gold quality |
| caecum | UBERON:0001153 | 69.49 | gold quality |
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 69.46 | gold quality |
| metanephros cortex | UBERON:0010533 | 69.46 | gold quality |
| pituitary gland | UBERON:0000007 | 69.25 | gold quality |
| adenohypophysis | UBERON:0002196 | 69.20 | gold quality |
| left ovary | UBERON:0002119 | 69.05 | gold quality |
| occipital lobe | UBERON:0002021 | 68.91 | gold quality |
| kidney | UBERON:0002113 | 68.77 | gold quality |
| right uterine tube | UBERON:0001302 | 68.73 | gold quality |
| bone marrow cell | CL:0002092 | 67.83 | gold quality |
| left uterine tube | UBERON:0001303 | 67.76 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 67.76 | gold quality |
| body of uterus | UBERON:0009853 | 67.76 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 67.74 | gold quality |
| bone marrow | UBERON:0002371 | 67.31 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 66.96 | gold quality |
| anatomical system | UBERON:0000467 | 66.79 | gold quality |
| body of pancreas | UBERON:0001150 | 66.77 | gold quality |
| material anatomical entity | UBERON:0000465 | 66.54 | gold quality |
| multicellular organism | UBERON:0000468 | 66.54 | gold quality |
| body of tongue | UBERON:0011876 | 66.47 | gold quality |
| thyroid gland | UBERON:0002046 | 66.13 | gold quality |
| tongue | UBERON:0001723 | 66.10 | silver quality |
| superior surface of tongue | UBERON:0007371 | 65.99 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 65.98 | gold quality |
| ectocervix | UBERON:0012249 | 65.97 | gold quality |
| saphenous vein | UBERON:0007318 | 65.95 | gold quality |
| trachea | UBERON:0003126 | 65.65 | gold quality |
| thymus | UBERON:0002370 | 65.64 | silver quality |
| ventral tegmental area | UBERON:0002691 | 65.62 | gold quality |
| lateral globus pallidus | UBERON:0002476 | 65.53 | gold quality |
| pancreas | UBERON:0001264 | 65.51 | gold quality |
| subthalamic nucleus | UBERON:0001906 | 65.50 | gold quality |
| islet of Langerhans | UBERON:0000006 | 65.45 | gold quality |
| pericardium | UBERON:0002407 | 65.39 | gold quality |
| skin of abdomen | UBERON:0001416 | 65.37 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 0.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 1.54 |
HPA expression
RNA tissue specificity: Tissue enhanced
showing 60 of 75 HPA tissues / cells by nTPM:
| Tissue / cell | Axis | nTPM |
|---|---|---|
| Heart muscle | tissue | 22.8 |
| Testis | tissue | 7.9 |
| Seminal vesicle | tissue | 7.6 |
| Nucleus accumbens | tissue | 5.5 |
| Tonsil | tissue | 5.5 |
| Lymph node | tissue | 5.1 |
| Hippocampus | tissue | 4.5 |
| Liver | tissue | 3.8 |
| Prostate | tissue | 3.3 |
| Postcentral gyrus | tissue | 3.2 |
| Spleen | tissue | 2.6 |
| Locus coeruleus | tissue | 2.5 |
| Bone marrow | tissue | 2.4 |
| Pituitary gland | tissue | 2.3 |
| Retina | tissue | 2.3 |
| Kidney | tissue | 2.0 |
| Parathyroid gland | tissue | 1.9 |
| Duodenum | tissue | 1.9 |
| Small intestine | tissue | 1.8 |
| Skin 1 | tissue | 1.7 |
| Appendix | tissue | 1.6 |
| Epididymis | tissue | 1.5 |
| Thymus | tissue | 1.5 |
| Vagina | tissue | 1.4 |
| Choroid plexus | tissue | 1.4 |
| Cerebral cortex | tissue | 1.2 |
| Temporal cortex | tissue | 1.2 |
| Basal ganglia | tissue | 1.1 |
| Retrosplenial cortex | tissue | 1.1 |
| Occipital cortex | tissue | 1.1 |
| Amygdala | tissue | 1.0 |
| Prefrontal cortex | tissue | 0.9 |
| Insular cortex | tissue | 0.9 |
| Ovary | tissue | 0.8 |
| Motor cortex | tissue | 0.8 |
| Putamen | tissue | 0.8 |
| Hippocampal formation | tissue | 0.8 |
| Entorhinal cortex | tissue | 0.8 |
| Periaqueductal gray | tissue | 0.8 |
| Endometrium 1 | tissue | 0.7 |
| Hypothalamus | tissue | 0.7 |
| Ventral forebrain | tissue | 0.7 |
| Retrosplenial and cingulate cortex | tissue | 0.7 |
| Olfactory bulb | tissue | 0.7 |
| Fallopian tube | tissue | 0.7 |
| Smooth muscle | tissue | 0.6 |
| Cerebellum | tissue | 0.6 |
| Gallbladder | tissue | 0.6 |
| Septum | tissue | 0.6 |
| Somatosensory cortex | tissue | 0.6 |
| Salivary gland | tissue | 0.5 |
| Colon | tissue | 0.5 |
| Medulla oblongata | tissue | 0.5 |
| Breast | tissue | 0.4 |
| Rectum | tissue | 0.4 |
| Skeletal muscle | tissue | 0.4 |
| Midbrain | tissue | 0.4 |
| Superior colliculi | tissue | 0.4 |
| Spinal cord | tissue | 0.4 |
| Adrenal gland | tissue | 0.4 |
Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Flocculonodular lobe (8.1), Vermis (7.9), Cerebellar cortex (7.2), Paraventricular nucleus (6.6), Supramarginal gyrus (6.3).
Regulation
Is transcription factor: no
Functional genomics
gnomAD constraint: pLI 1.71e-06, LOEUF 1.04, missense Z -0.0122 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD
Regional missense constraint (gnomAD RMC): no regional variation along ENST00000372569 — one region, missense o/e 1.01.
Literature-anchored findings (GeneRIF, showing 1)
- TLP-mediated global transcriptional repression after double-strand DNA breaks slows down DNA repair and induces apoptosis. (PMID:30890736)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | crip3 | ENSDARG00000043395 |
| mus_musculus | Crip3 | ENSMUSG00000023968 |
| rattus_norvegicus | Crip3 | ENSRNOG00000018613 |
Paralogs (20): FHL1 (ENSG00000022267), LMO3 (ENSG00000048540), LHX5 (ENSG00000089116), ZFHX4 (ENSG00000091656), LHX2 (ENSG00000106689), LHX6 (ENSG00000106852), LHX3 (ENSG00000107187), LHX4 (ENSG00000121454), LMO2 (ENSG00000135363), ZFHX2 (ENSG00000136367), LMX1B (ENSG00000136944), ZFHX3 (ENSG00000140836), LMO4 (ENSG00000143013), LHX9 (ENSG00000143355), LHX8 (ENSG00000162624), LMX1A (ENSG00000162761), LMO1 (ENSG00000166407), CRIP2 (ENSG00000182809), CRIP1 (ENSG00000213145), LHX1 (ENSG00000273706)
Mouse-model phenotypes
Observed phenotypes of the mouse ortholog (MGI:2152434) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 4 distinct phenotype terms.
| Mouse phenotype (MP) | Records |
|---|---|
| small thymus | 1 |
| decreased thymocyte number | 1 |
| decreased exploration in new environment | 1 |
| thymus hypoplasia | 1 |
Additional cross-species homologs
Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.
| Organism | UniProt | Identity | Method |
|---|---|---|---|
| Gallus gallus | P67966 | 100.0% | Diamond |
| Coturnix japonica | P67967 | 100.0% | Diamond |
| Bos taurus | Q32LE9 | 100.0% | Diamond |
| Pongo abelii | Q5RCT4 | 99.5% | Diamond |
| Drosophila melanogaster | Q24400 | 76.7% | Diamond |
| Helianthus annuus | P29675 | 72.0% | Diamond |
| Dictyostelium discoideum | Q9BIW5 | 45.2% | Diamond |
Genomic neighbors (locus context)
Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).
| Symbol | Type | Entrez |
|---|---|---|
| SLC22A7 | protein-coding | 10864 |
| ZNF318 | protein-coding | 24149 |
| DNPH1 | protein-coding | 10591 |
| TTBK1 | protein-coding | 84630 |
| CUL9 | protein-coding | 23113 |
Protein
Protein identifiers
Cysteine-rich protein 3 — Q6Q6R5 (reviewed: Q6Q6R5)
Alternative names: Chromosome 6 LIM domain only protein
All UniProt accessions (3): Q6Q6R5, H0Y7Q9, Q5T045
UniProt curated annotations — full annotation on UniProt →
Subcellular location. Cytoplasm.
Tissue specificity. Expressed in most tissues, but not in skeletal muscle.
Isoforms (4)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q6Q6R5-1 | 1, C | yes |
| Q6Q6R5-2 | 2, B | |
| Q6Q6R5-3 | 3, A | |
| Q6Q6R5-4 | 4, D |
RefSeq proteins (2): NP_001352997, NP_996805* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001781 | Znf_LIM | Domain |
Pfam: PF00412
UniProt features (9 total): splice variant 3, domain 2, sequence conflict 2, chain 1, region of interest 1
Structure
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q6Q6R5-F1 | 74.81 | 0.42 |
Human Protein Atlas
Protein class: Predicted intracellular proteins
Protein evidence: Evidence at protein level
Subcellular location (HPA, imaging): nuclear speckles
Antibody reliability (HPA): IH uncertain · IF approved
Function
Pathways and Gene Ontology
Reactome pathways
0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).
MSigDB gene sets: 44 (showing top):
GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, STK33_SKM_DN, ZNF322_TARGET_GENES, MIR4731_5P, GSE11057_EFF_MEM_VS_CENT_MEM_CD4_TCELL_DN, MIR423_5P, MIR3184_5P, MIR6759_3P, GSE12366_NAIVE_VS_MEMORY_BCELL_UP, MIR1911_5P, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN, GSE15750_WT_VS_TRAF6KO_DAY10_EFF_CD8_TCELL_UP, HAY_BONE_MARROW_DENDRITIC_CELL, GSE17721_POLYIC_VS_CPG_16H_BMDC_UP, WRNIP1_TARGET_GENES
GO Molecular Function (2): metal ion binding (GO:0046872), protein binding (GO:0005515)
GO Cellular Component (1): cytoplasm (GO:0005737)
GO top-level categories
4 GO namespaces:
| Category | Terms |
|---|---|
| cation binding | 1 |
| binding | 1 |
| intracellular anatomical structure | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
showing 16 of 234 interactions by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CRIP3 | HOXD8 | P13378 | 390 |
| CRIP3 | CLRN2 | A0PK11 | 380 |
| CRIP3 | SCO1 | O75880 | 378 |
| CRIP3 | SMIM12 | Q96EX1 | 366 |
| CRIP3 | BEND7 | Q8N7W2 | 339 |
| CRIP3 | TCAIM | Q8N3R3 | 330 |
| CRIP3 | H0YIS7 | H0YIS7 | 315 |
| CRIP3 | LRRC40 | Q9H9A6 | 314 |
| CRIP3 | HOXD3 | P31249 | 314 |
| CRIP3 | MNMIP1 | A4FU49 | 307 |
| CRIP3 | COA6 | Q5JTJ3 | 306 |
| CRIP3 | TMEM128 | Q5BJH2 | 295 |
| CRIP3 | BTBD8 | Q5XKL5 | 286 |
| CRIP3 | BAIAP2L2 | Q6UXY1 | 286 |
| CRIP3 | TMEM179 | Q6ZVK1 | 286 |
| CRIP3 | KLHDC7B | Q96G42 | 286 |
IntAct
BioGRID (2 interactions; top human partners by supporting records): FHL3 (Two-hybrid), PLOD3 (Two-hybrid)
Disease & clinical
Genetic variants
Variant evidence for CRIP3: 37 ClinVar records (0 pathogenic / likely pathogenic); 20 GWAS associations.
ClinVar
37 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 29 |
| Likely benign | 1 |
| Benign | 0 |
SpliceAI
Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 31 predictions of 758):
| Position(s) | Effect | Δscore | Sites |
|---|---|---|---|
| 6:43306125–43306126 | acceptor_loss | 0.9900 | 6 |
| 6:43306134 | acceptor_gain | 0.9900 | |
| 6:43306217–43306218 | donor_loss | 0.9900 | 4 |
| 6:43306314–43306315 | acceptor_loss | 0.9900 | 6 |
| 6:43306317 | acceptor_gain | 0.9900 | |
| 6:43306320 | acceptor_gain | 0.9900 | |
| 6:43306122 | acceptor_gain | 0.9800 | |
| 6:43306218 | donor_loss | 0.9800 | |
| 6:43306444–43306445 | donor_loss | 0.9800 | 5 |
| 6:43306518–43306519 | acceptor_loss | 0.9800 | 5 |
AlphaMissense
477 missense substitutions predicted likely pathogenic (of 1,340 scored), across 106 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:
| Residue | Likely-pathogenic substitutions | Mean am_pathogenicity | Max am_pathogenicity |
|---|---|---|---|
| H145 | 8 | 0.973 | 0.991 |
| H26 | 8 | 0.971 | 0.990 |
| H44 | 8 | 0.893 | 0.979 |
| H163 | 8 | 0.875 | 0.978 |
| W144 | 7 | 0.985 | 0.995 |
| W25 | 7 | 0.983 | 0.993 |
| C151 | 7 | 0.983 | 0.994 |
| C172 | 7 | 0.983 | 0.991 |
| C124 | 7 | 0.982 | 0.994 |
| C29 | 7 | 0.981 | 0.990 |
| C154 | 7 | 0.981 | 0.992 |
| C176 | 7 | 0.981 | 0.991 |
| C53 | 7 | 0.979 | 0.987 |
| C32 | 7 | 0.978 | 0.991 |
| C148 | 7 | 0.974 | 0.984 |
| C57 | 7 | 0.973 | 0.987 |
| C35 | 7 | 0.971 | 0.984 |
| F62 | 7 | 0.968 | 0.993 |
| C5 | 7 | 0.967 | 0.988 |
| F181 | 7 | 0.966 | 0.992 |
HPA cancer prognostics
RNA cancer specificity: Cancer enhanced (Kidney Chromophobe, Liver Hepatocellular Carcinoma)
Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.
1 prognostic cancer types:
| Cancer | Prognostic | p-value |
|---|---|---|
| Kidney Renal Papillary Cell Carcinoma (TCGA) | favorable | 0.000197 |
Disease associations
OMIM: gene `` | disease phenotypes:
GWAS associations
20 associations:
| Study | Trait | p-value |
|---|---|---|
| GCST005962_28 | Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test) | 3e-31 |
| GCST005956_15 | Waist-to-hip ratio adjusted for BMI | 7e-26 |
| GCST008899_1 | Adult hearing difficulty | 6e-21 |
| GCST006188_41 | Systolic blood pressure (cigarette smoking interaction) | 8e-21 |
| GCST008058_65 | Estimated glomerular filtration rate | 1e-20 |
| GCST008059_76 | Estimated glomerular filtration rate | 2e-20 |
| GCST005958_10 | Waist-to-hip ratio adjusted for BMI (age >50) | 2e-19 |
| GCST012442_45 | Age-related hearing impairment | 1e-17 |
| GCST005957_3 | Waist-to-hip ratio adjusted for BMI (age <50) | 2e-14 |
| GCST006187_17 | Diastolic blood pressure (cigarette smoking interaction) | 1e-10 |
| GCST007703_114 | Systolic blood pressure | 4e-10 |
| GCST007099_139 | Systolic blood pressure | 1e-9 |
| GCST007706_67 | Mean arterial pressure | 4e-9 |
| GCST012227_928 | Hip circumference adjusted for BMI | 2e-8 |
| GCST004521_115 | Autism spectrum disorder or schizophrenia | 3e-8 |
| GCST008839_556 | Height | 4e-8 |
| GCST007704_30 | Diastolic blood pressure | 1e-6 |
| GCST007707_27 | Hypertension | 1e-6 |
| GCST007096_130 | Pulse pressure | 3e-6 |
| GCST007705_94 | Pulse pressure | 4e-6 |
EFO canonical traits (from GWAS)
9 canonical traits:
| EFO ID | Trait name |
|---|---|
| EFO:0007788 | BMI-adjusted waist-hip ratio |
| EFO:0008007 | age at assessment |
| EFO:0008343 | sex interaction measurement |
| EFO:0006336 | diastolic blood pressure |
| EFO:0006527 | smoking status measurement |
| EFO:0006335 | systolic blood pressure |
| EFO:0005763 | pulse pressure measurement |
| EFO:0006340 | mean arterial pressure |
| EFO:0008039 | BMI-adjusted hip circumference |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (CPIC guideline: no)
CTD chemical–gene interactions
26 total (human), top 26 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | decreases expression, decreases methylation | 2 |
| Aflatoxin B1 | decreases expression | 2 |
| propionaldehyde | increases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| pentanal | increases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| abrine | decreases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| jinfukang | increases expression, affects cotreatment | 1 |
| Resveratrol | decreases expression, affects cotreatment | 1 |
| Sunitinib | increases expression | 1 |
| Leflunomide | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Cisplatin | affects cotreatment, increases expression | 1 |
| Copper | affects cotreatment, decreases expression | 1 |
| Diethylhexyl Phthalate | decreases expression | 1 |
| N-Nitrosopyrrolidine | decreases expression | 1 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 1 |
| Silicon Dioxide | decreases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
| Urethane | decreases expression | 1 |
| Valproic Acid | affects expression | 1 |
| Cyclosporine | decreases methylation | 1 |
| Okadaic Acid | decreases expression | 1 |
| Copper Sulfate | decreases expression | 1 |
Clinical trials (associated diseases)
Via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hypertensive disorder, presbycusis