TMEM67

gene
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Also known as MGC26979JBTS6NPHP11

Summary

TMEM67 (transmembrane protein 67, HGNC:28396) is a protein-coding gene on chromosome 8q22.1, encoding Meckelin (Q5HYA8). Required for ciliary structure and function.

The protein encoded by this gene localizes to the primary cilium and to the plasma membrane. The gene functions in centriole migration to the apical membrane and formation of the primary cilium. Multiple transcript variants encoding different isoforms have been found for this gene. Defects in this gene are a cause of Meckel syndrome type 3 (MKS3) and Joubert syndrome type 6 (JBTS6).

Source: NCBI Gene 91147 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): ciliopathy (Definitive, ClinGen) — +7 more curated relationships
  • Clinical variants (ClinVar): 1,433 total — 117 pathogenic, 88 likely-pathogenic
  • Phenotypes (HPO): 193
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_153704

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28396
Approved symbolTMEM67
Nametransmembrane protein 67
Location8q22.1
Locus typegene with protein product
StatusApproved
AliasesMGC26979, JBTS6, NPHP11
Ensembl geneENSG00000164953
Ensembl biotypeprotein_coding
OMIM609884
Entrez91147

Gene structure

Transcript identifiers

Ensembl transcripts: 47 — 19 nonsense_mediated_decay, 13 protein_coding, 12 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000323130, ENST00000409623, ENST00000425545, ENST00000452276, ENST00000453321, ENST00000453906, ENST00000455946, ENST00000474944, ENST00000475305, ENST00000481620, ENST00000496213, ENST00000498673, ENST00000518319, ENST00000518896, ENST00000519845, ENST00000520680, ENST00000521065, ENST00000521222, ENST00000521517, ENST00000523230, ENST00000681998, ENST00000682036, ENST00000682577, ENST00000682624, ENST00000682700, ENST00000682744, ENST00000682804, ENST00000682837, ENST00000682935, ENST00000682984, ENST00000683078, ENST00000683223, ENST00000683238, ENST00000683249, ENST00000683336, ENST00000683362, ENST00000683850, ENST00000683919, ENST00000683953, ENST00000684023, ENST00000684064, ENST00000684089, ENST00000684149, ENST00000684343, ENST00000684416, ENST00000684540, ENST00000684733

RefSeq mRNA: 2 — MANE Select: NM_153704 NM_001142301, NM_153704

CCDS: CCDS6258

Canonical transcript exons

ENST00000453321 — 28 exons

ExonStartEnd
ENSE000017630189378239593782460
ENSE000017848869376557293765646
ENSE000021032959375489493755137
ENSE000021078369381637293818121
ENSE000034585989379733193797470
ENSE000034586459376540693765475
ENSE000034647639378522293785378
ENSE000034675049380905793809161
ENSE000034692189378622393786346
ENSE000034822269379126393791319
ENSE000034910839375848393758576
ENSE000034928189379540993795507
ENSE000034938529380476293804878
ENSE000035144199378087493780982
ENSE000035201359375577893755866
ENSE000035465839378165893781744
ENSE000035500829377258993772651
ENSE000035531749378784493787949
ENSE000035539159380360493803684
ENSE000035672789379713493797233
ENSE000035683129379590193795987
ENSE000035686529380978593809887
ENSE000036236229379961893799758
ENSE000036271949376384293763941
ENSE000036309719379319893793296
ENSE000036348269378059393780747
ENSE000036424959380884093808956
ENSE000036859059381530593815447

Expression profiles

Bgee: expression breadth ubiquitous, 203 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4226 / max 80.7828, expressed in 1635 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
897577.02381622
897560.3646172
897580.03428

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233697.85gold quality
right uterine tubeUBERON:000130294.98gold quality
calcaneal tendonUBERON:000370192.20gold quality
bronchial epithelial cellCL:000232890.96gold quality
olfactory segment of nasal mucosaUBERON:000538690.40gold quality
ventricular zoneUBERON:000305389.84gold quality
bronchusUBERON:000218589.55gold quality
heart left ventricleUBERON:000208487.58gold quality
tendonUBERON:000004387.38gold quality
adenohypophysisUBERON:000219687.38gold quality
adrenal tissueUBERON:001830387.35gold quality
oviduct epitheliumUBERON:000480487.29gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099187.14gold quality
cardiac ventricleUBERON:000208286.91gold quality
left testisUBERON:000453386.87gold quality
right testisUBERON:000453486.68gold quality
mucosa of paranasal sinusUBERON:000503086.34gold quality
pituitary glandUBERON:000000786.04gold quality
spermCL:000001985.95gold quality
right atrium auricular regionUBERON:000663185.88gold quality
apex of heartUBERON:000209885.80gold quality
testisUBERON:000047385.71gold quality
heartUBERON:000094885.53gold quality
fallopian tubeUBERON:000388985.51gold quality
left lobe of thyroid glandUBERON:000112085.28gold quality
thyroid glandUBERON:000204685.11gold quality
right lobe of thyroid glandUBERON:000111984.82gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.70gold quality
cardiac atriumUBERON:000208184.70gold quality
left ovaryUBERON:000211984.01gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-114yes11.08
E-ANND-3yes10.21
E-GEOD-124858no153.61
E-MTAB-7381no144.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

94 targeting TMEM67, 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-5692A100.0074.406850
HSA-MIR-8485100.0077.574731
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-428299.9975.366408
HSA-MIR-366299.9973.825684
HSA-MIR-118499.9968.191458
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-1213699.9872.815713
HSA-MIR-806899.9873.852376
HSA-MIR-56899.9869.862084
HSA-MIR-50799.9770.111915
HSA-MIR-548AN99.9770.912817
HSA-MIR-55799.9670.011640
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-144-3P99.9473.982698
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-6768-5P99.9267.361942

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 25)

  • mapping to chromosome 8 and possible role in Meckel-Gruber syndrome (PMID:12384791)
  • Positional cloning of the Wpk gene suggested a MKS3 candidate gene, TMEM67, for which we identified pathogenic mutations for five MKS3-linked consanguineous families. (PMID:16415887)
  • identified MKS3 mutations in four patients with JS, thus defining MKS3 as the sixth JS locus (JBTS6) (PMID:17160906)
  • The Meckel-Gruber Syndrome proteins MKS1 and meckelin interact and are required for primary cilium formation. (PMID:17185389)
  • Study concluded that MKS1 and MKS3 account for the majority of Meckel-Gruber syndrome; polydactyly is usually found in MKS1 but rare in MKS3; cases with no, or milder, CNS phenotypes were only found in MKS3. (PMID:17377820)
  • genotyping of MKS1 & MKS3 genes in a large, multiethnic cohort of 120 independent cases of Meckel syndrome; first results indicate that the MKS1 & MKS3 genes are each responsible for about 7% of MKS cases with various mutations in different populations (PMID:17397051)
  • Mutations in MKS3 is associated with Bardet-Biedl syndrome (PMID:18327255)
  • Analysis of MKS3 in 14 COACH families identified mutations in 8 (57%). (PMID:19058225)
  • Missense mutations within the MKS3 gene are associated with nephronophthisis with liver fibrosis. (PMID:19508969)
  • Kidney tissue and cells from MKS1 and MKS3 patients showed defects in centrosome and cilia number, including multi-ciliated respiratory-like epithelia, and longer cilia. (PMID:19515853)
  • Mutations in MKS3 are responsible for the majority of COACH syndrome, with minor contributions from CC2D2A and RPGRIP1L. (PMID:19574260)
  • Data show that knockdown of MKS3 inhibited degradation of mutant SP-C. (PMID:19815549)
  • mutation analysis of TMEM67 in Joubert syndrome and related disorders cases and Meckel syndrome fetuses; identification of 20 novel mutations; review of published mutations and discussion of genotype-phenotype correlates (PMID:20232449)
  • The Meckel syndrome protein meckelin (TMEM67) is a key regulator of cilia function but is not required for tissue planar polarity. (PMID:23393159)
  • Importantly, one Japanese and one Omani families carried compound biallelic mutations in two distinct genes (TMEM67/RPGRIP1L and TMEM138/BBS1, respectively). (PMID:27434533)
  • Low expression of TMEM67 is associated with lymph node metastasis in urothelial carcinoma of the bladder. (PMID:28161324)
  • The authors results suggest that Asn242Ser in TMEM67 is a founder mutation in the Iranian population, which might explain a significant proportion of JS cases from eastern Iran. (PMID:28719906)
  • Study identified two novel heterozygous mutations (p.Gly132Ala and p.Tyr920ThrfsX40) in the TMEM67 gene in a patient with COACH syndrome. Co-injection into zebrafish embryos of tmem67 morpholinos and RNAs encoding the two mutations show no rescue of the hydrocephalus phenotype. These findings indicate that the two mutations may cause COACH syndrome via altered Wnt signaling, at least in part. (PMID:28860541)
  • Kidney disease occurs in up to one third of patients with Joubert syndrome, most commonly in those with mutations in CEP290, TMEM67, and AHI1. (PMID:29146704)
  • Compound heterozygous mutations in TMEM67 cause RHYNS syndrome ranging from early lethality to adults with liver fibrosis. (PMID:29891882)
  • This study confirms the diagnosis of Joubert syndrome in a Vietnamese family and expands the mutational spectrum of TMEM67 sequence variations. (PMID:32000717)
  • TACC3 promotes prostate cancer cell proliferation and restrains primary cilium formation. (PMID:32156598)
  • Association of novel TMEM67 variants with mild phenotypes of high gamma-glutamyl transpeptidase cholestasis and congenital hepatic fibrosis. (PMID:35621037)
  • TMEM67 is required for the gating function of the transition zone that controls entry of membrane-associated proteins ARL13B and INPP5E into primary cilia. (PMID:36334440)
  • Two novel TMEM67 variations in a Chinese family with recurrent pregnancy loss: a case report. (PMID:38844949)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotmem67ENSDARG00000076752
mus_musculusTmem67ENSMUSG00000049488
rattus_norvegicusTmem67ENSRNOG00000016187
drosophila_melanogasterCG15923FBGN0038814
caenorhabditis_elegansWBGENE00018042

Protein

Protein identifiers

MeckelinQ5HYA8 (reviewed: Q5HYA8)

Alternative names: Meckel syndrome type 3 protein, Transmembrane protein 67

All UniProt accessions (20): A0A0C4DFP8, A0A7P0MXI9, A0A804HHW8, A0A804HIB2, A0A804HJR8, Q5HYA8, A0A804HJS5, A0A804HJX6, A0A804HKM4, A0A804HKM9, A0A804HL43, A0A804HLK0, C9JHI2, C9JRQ8, E5RG10, E5RH38, F8WCQ6, H0YAR5, H0YB69, H0YC18

UniProt curated annotations — full annotation on UniProt →

Function. Required for ciliary structure and function. Part of the tectonic-like complex which is required for tissue-specific ciliogenesis and may regulate ciliary membrane composition. Involved in centrosome migration to the apical cell surface during early ciliogenesis. Involved in the regulation of cilia length and appropriate number through the control of centrosome duplication. Is a key regulator of stereociliary bundle orientation. Required for epithelial cell branching morphology. Essential for endoplasmic reticulum-associated degradation (ERAD) of surfactant protein C (SFTPC). Involved in the negative regulation of canonical Wnt signaling, and activation of the non-canonical cascade stimulated by WNT5A. In non-canonical Wnt signaling, it may act as ROR2 coreceptor.

Subunit / interactions. Homodimer. Part of the tectonic-like complex (also named B9 complex). Interacts with DNAJB9, DNAJC10 and mutated SFTPC. Interacts with SYNE2 during the early establishment of cell polarity. Interacts (via C-terminus) with FLNA. Interacts with TMEM218. Interacts with WNT5A. Interacts with ROR2.

Subcellular location. Cell membrane. Endoplasmic reticulum membrane. Cell projection. Cilium. Cytoplasm. Cytoskeleton. Cilium basal body.

Tissue specificity. Widely expressed in adult and fetal tissues. Expressed at higher level in spinal cord.

Disease relevance. TMEM67 mutations result in ciliary dysfunction leading to a broad spectrum of disorders, collectively termed ciliopathies. Overlapping clinical features include retinal degeneration, renal cystic disease, skeletal abnormalities, fibrosis of various organ, and a complex range of anatomical and functional defects of the central and peripheral nervous system. The ciliopathy range of diseases includes Meckel-Gruber syndrome, Bardet-Biedl syndrome, Joubert syndrome, and nephronophtisis among others. Single-locus allelism is insufficient to explain the variable penetrance and expressivity of such disorders, leading to the suggestion that variations across multiple sites of the ciliary proteome influence the clinical outcome. Meckel syndrome 3 (MKS3) [MIM:607361] A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. The disease is caused by variants affecting the gene represented in this entry. Joubert syndrome 6 (JBTS6) [MIM:610688] A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. The disease is caused by variants affecting the gene represented in this entry. Bardet-Biedl syndrome 14 (BBS14) [MIM:615991] A syndrome characterized by usually severe pigmentary retinopathy, early-onset obesity, polydactyly, hypogenitalism, renal malformation and intellectual disability. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. The gene represented in this entry may act as a disease modifier. TMEM67 variations may influence the expression of Bardet-Biedl syndrome in patients who have causative mutations in other genes. Heterozygosity for a complex mutation in the TMEM67 gene coding for a protein with 2 in cis changes, and homozygosity for a truncating mutation of the CEP290 gene has been found in a patient with Bardet-Biedl syndrome 14. COACH syndrome 1 (COACH1) [MIM:216360] A form of COACH syndrome, a disorder characterized by cerebellar vermis hypoplasia, developmental delay, impaired intellectual development, ataxia, and hepatic fibrosis. Patients present the molar tooth sign, a midbrain-hindbrain malformation pathognomonic for Joubert syndrome and related disorders. Other features, such as coloboma and renal cysts, may be variable. COACH1 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry. Nephronophthisis 11 (NPHP11) [MIM:613550] A disorder characterized by the association of nephronophthisis with hepatic fibrosis. Nephronophthisis is a progressive tubulo-interstitial kidney disorder histologically characterized by modifications of the tubules with thickening of the basement membrane, interstitial fibrosis and, in the advanced stages, medullary cysts. Typical clinical features are chronic renal failure, anemia, polyuria, polydipsia, isosthenuria, and growth retardation. Associations with extrarenal symptoms, especially ocular lesions, are frequent. The disease is caused by variants affecting the gene represented in this entry. RHYNS syndrome (RHYNS) [MIM:602152] An autosomal recessive syndrome characterized by gaze palsy, retinitis pigmentosa, sensorineural hearing loss, hypopituitarism, nephronophthisis, and skeletal dysplasia. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (2): NP_001135773, NP_714915* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009030Growth_fac_rcpt_cys_sfHomologous_superfamily
IPR019170MeckelinFamily

Pfam: PF09773

UniProt features (181 total): sequence variant 58, strand 44, helix 24, disulfide bond 12, intramembrane region 9, topological domain 8, transmembrane region 7, turn 5, mutagenesis site 4, glycosylation site 4, sequence conflict 2, signal peptide 1, chain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
7FH1ELECTRON MICROSCOPY3.34

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5HYA8-F185.200.47

Functional residue map

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

Disulfide bonds (12): 49–62, 65–78, 80–97, 100–114, 117–127, 129–150, 153–170, 173–184, 186–197, 237–246, 253–268, 357–378

Glycosylation sites (4): 141, 179, 242, 318

Mutagenesis-validated functional residues (4):

PositionPhenotype
170decreased function in non-canonical wnt signaling activation. when expressed in tmem67-null cells does not induce ror2 p
176does not affect function in non-canonical wnt signaling activation. when expressed in tmem67-null cells it induces ror2
790decreased function in non-canonical wnt signaling activation. when expressed in tmem67-null cells does not induce ror2 p
979does not affect function in non-canonical wnt signaling activation. when expressed in tmem67-null cells it induces ror2

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-5620912Anchoring of the basal body to the plasma membrane
R-HSA-1852241Organelle biogenesis and maintenance
R-HSA-5617833Cilium Assembly

MSigDB gene sets: 504 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_NON_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_CILIUM_ORGANIZATION, GOBP_REGULATION_OF_CELL_CYCLE, GOCC_CENTROSOME, GOBP_REGULATION_OF_CENTROSOME_CYCLE, GOBP_ORGANELLE_ASSEMBLY

GO Biological Process (5): negative regulation of centrosome duplication (GO:0010826), non-canonical Wnt signaling pathway (GO:0035567), ERAD pathway (GO:0036503), cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (3): filamin binding (GO:0031005), obsolete unfolded protein binding (GO:0051082), protein binding (GO:0005515)

GO Cellular Component (13): endoplasmic reticulum membrane (GO:0005789), centrosome (GO:0005813), cytoplasmic vesicle membrane (GO:0030659), ciliary transition zone (GO:0035869), MKS complex (GO:0036038), ciliary membrane (GO:0060170), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cilium (GO:0005929), membrane (GO:0016020), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Assembly of the 9+0 primary cilium1
Organelle biogenesis and maintenance1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cilium2
regulation of centrosome duplication1
negative regulation of centrosome cycle1
centrosome duplication1
Wnt signaling pathway1
proteasomal protein catabolic process1
response to endoplasmic reticulum stress1
response to chemical1
axoneme assembly1
intraciliary transport involved in cilium assembly1
cilium organization1
protein localization to cilium1
organelle assembly1
trans-Golgi to periciliary membrane compartment transport1
plasma membrane bounded cell projection assembly1
ciliary transition zone assembly1
cellular component organization1
cytoskeletal protein binding1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
centriole1
microtubule organizing center1
vesicle membrane1
cytoplasmic vesicle1
protein-containing complex1
ciliary transition zone1
cell projection membrane1
bounding membrane of organelle1
intracellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
membrane1
cell periphery1
intraciliary transport particle1
membrane-bounded organelle1

Protein interactions and networks

STRING

924 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMEM67TMEM216Q9P0N5994
TMEM67NPHP1O15259992
TMEM67CEP290O15078991
TMEM67CC2D2AQ9P2K1990
TMEM67B9D1Q9UPM9987
TMEM67MKS1Q9NXB0987
TMEM67B9D2Q9BPU9975
TMEM67TMEM231Q9H6L2973
TMEM67RPGRIP1LQ68CZ1970
TMEM67TCTN2Q96GX1968
TMEM67TCTN1Q2MV58968
TMEM67AHI1Q8N157967
TMEM67NPHP4O75161967
TMEM67TMEM237Q96Q45939
TMEM67TCTN3Q6NUS6925

IntAct

105 interactions, top by confidence:

ABTypeScore
CD27TCAF2psi-mi:“MI:0914”(association)0.640
TMEM67APPpsi-mi:“MI:0915”(physical association)0.560
SCGB1D1FAM234Bpsi-mi:“MI:0914”(association)0.530
TMEM30BKLRG2psi-mi:“MI:0914”(association)0.530
SPINK4PLXNA2psi-mi:“MI:0914”(association)0.530
DEFA1MANBApsi-mi:“MI:0914”(association)0.530
TAFA4NRP1psi-mi:“MI:0914”(association)0.530
CD1ESUSD5psi-mi:“MI:0914”(association)0.530
TCTN2TPST2psi-mi:“MI:0914”(association)0.530
ADAM33LRP5psi-mi:“MI:0914”(association)0.530
SCGB1D4EGFRpsi-mi:“MI:0914”(association)0.530
DEFB121COL6A2psi-mi:“MI:0914”(association)0.530
SLC22A9GPR89Apsi-mi:“MI:0914”(association)0.530
CLGNNPC1psi-mi:“MI:0914”(association)0.530
NRN1SLC1A1psi-mi:“MI:0914”(association)0.530
CD70METTL15psi-mi:“MI:0914”(association)0.530
TMPRSS11Bpsi-mi:“MI:0914”(association)0.350
TMEM30AUPK3BL1psi-mi:“MI:0914”(association)0.350
LYPD3CLASP2psi-mi:“MI:0914”(association)0.350
SLC22A9GPR89Apsi-mi:“MI:0914”(association)0.350
PTPRKMANBApsi-mi:“MI:0914”(association)0.350

BioGRID (165): TMEM67 (Affinity Capture-MS), TMEM67 (Affinity Capture-MS), TMEM67 (Affinity Capture-MS), TMEM67 (Affinity Capture-MS), ABCD3 (Proximity Label-MS), AKAP1 (Proximity Label-MS), ATP6AP1 (Proximity Label-MS), ATP6AP2 (Proximity Label-MS), ATP6V0A1 (Proximity Label-MS), CAMLG (Proximity Label-MS), CCDC47 (Proximity Label-MS), CKAP4 (Proximity Label-MS), DDX54 (Proximity Label-MS), ERLIN2 (Proximity Label-MS), HM13 (Proximity Label-MS)

ESM2 similar proteins: A5PJN2, B1H1F9, B4URD6, B6CVD7, O18823, O43556, O43909, O56140, O70258, P0C152, P28039, P97259, Q01H84, Q08834, Q09328, Q28F39, Q29S03, Q2F4V2, Q4R5B1, Q5HYA8, Q5RAP2, Q6AXF6, Q6DD71, Q6DPZ9, Q6DQ19, Q6DQ21, Q6J8E7, Q6YAT4, Q7SEY9, Q7T3D1, Q7X9I4, Q7YTU4, Q86YB8, Q8BR76, Q8IZ81, Q8NBP0, Q8QPL1, Q8R180, Q8R2E9, Q8R3N6

Diamond homologs: P0C152, Q5HYA8, Q8BR76

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 136 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Antigen Presentation: Folding, assembly and peptide loading of class I MHC627.5×3e-05
Beta defensins619.0×1e-04
Defensins616.6×2e-04
Interferon gamma signaling710.2×5e-04
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell88.1×5e-04

GO biological processes:

GO termPartnersFoldFDR
peptide antigen assembly with MHC class II protein complex545.0×3e-05
positive regulation of T cell mediated cytotoxicity834.9×5e-08
antigen processing and presentation of exogenous peptide antigen via MHC class II523.2×4e-04
positive regulation of immune response520.6×5e-04
positive regulation of T cell activation518.9×7e-04
defense response to Gram-negative bacterium68.6×3e-03
adaptive immune response96.5×1e-03
immune response114.4×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1433 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic117
Likely pathogenic88
Uncertain significance497
Likely benign515
Benign52

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1065634NM_153704.6(TMEM67):c.230C>A (p.Ser77Ter)Pathogenic
1073371NM_153704.6(TMEM67):c.2087T>C (p.Leu696Pro)Pathogenic
1252092NM_153704.6(TMEM67):c.2306del (p.Leu769fs)Pathogenic
1252093NM_153704.6(TMEM67):c.2439G>A (p.Ala813=)Pathogenic
1252094NM_153704.6(TMEM67):c.2326T>A (p.Ser776Thr)Pathogenic
1319812NM_153704.6(TMEM67):c.1960+2T>CPathogenic
1323695NM_153704.6(TMEM67):c.1289-2delPathogenic
1352682NM_153704.6(TMEM67):c.714G>A (p.Trp238Ter)Pathogenic
1368NM_153704.6(TMEM67):c.2315_2322+4delinsGPathogenic
1369NM_153704.6(TMEM67):c.1127A>C (p.Gln376Pro)Pathogenic
1372NM_153704.6(TMEM67):c.2439+5G>CPathogenic
1374490NM_153704.6(TMEM67):c.459T>A (p.Cys153Ter)Pathogenic
1375NM_153704.6(TMEM67):c.1961-2A>CPathogenic
1376NM_153704.6(TMEM67):c.622A>T (p.Arg208Ter)Pathogenic
1377709NM_153704.6(TMEM67):c.683_689del (p.Lys228fs)Pathogenic
1379NM_153704.6(TMEM67):c.2556+1G>TPathogenic
1380NM_153704.6(TMEM67):c.312+5G>APathogenic
1382NM_153704.6(TMEM67):c.2461G>A (p.Gly821Ser)Pathogenic
1384NM_153704.6(TMEM67):c.869G>T (p.Trp290Leu)Pathogenic
1385NM_153704.6(TMEM67):c.2461G>C (p.Gly821Arg)Pathogenic
1386NM_153704.6(TMEM67):c.130C>T (p.Gln44Ter)Pathogenic
1390145NM_153704.6(TMEM67):c.1638del (p.Gly545_Trp546insTer)Pathogenic
1394423NM_153704.6(TMEM67):c.312+2T>GPathogenic
1411457NM_153704.6(TMEM67):c.1387C>T (p.Arg463Ter)Pathogenic
1433508NM_153704.6(TMEM67):c.924_925insTGAGGAGTGTCTCTGCCCGGCCGCTCCGTCTGAGAAGTGAGGAAACCCTCTGCCTGGCAACCGCCCCGTCTGAGAAGTGAGGAGCCCCTCCGTNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAGGATTAGCACCTCAA (p.Val309Ter)Pathogenic
1453206NM_153704.6(TMEM67):c.1638G>A (p.Trp546Ter)Pathogenic
1454299NM_153704.6(TMEM67):c.1927C>T (p.Arg643Ter)Pathogenic
1454745NM_153704.6(TMEM67):c.996_1014del (p.Phe332fs)Pathogenic
1456259NC_000008.10:g.(?94821048)(94822135_?)delPathogenic
1458833NM_153704.6(TMEM67):c.2345A>G (p.His782Arg)Pathogenic

SpliceAI

4566 predictions. Top by Δscore:

VariantEffectΔscore
8:93755135:GAG:Gdonor_gain1.0000
8:93755138:G:GGdonor_gain1.0000
8:93755138:GTAAG:Gdonor_loss1.0000
8:93755906:GTA:Gdonor_gain1.0000
8:93763831:A:AGacceptor_gain1.0000
8:93763832:A:Gacceptor_gain1.0000
8:93765476:G:GGdonor_gain1.0000
8:93772583:TTACA:Tacceptor_loss1.0000
8:93772584:TACA:Tacceptor_loss1.0000
8:93772586:CA:Cacceptor_loss1.0000
8:93772587:A:AGacceptor_gain1.0000
8:93772587:A:Cacceptor_loss1.0000
8:93772587:AG:Aacceptor_gain1.0000
8:93772587:AGG:Aacceptor_gain1.0000
8:93772588:G:GAacceptor_gain1.0000
8:93772588:GG:Gacceptor_gain1.0000
8:93772588:GGG:Gacceptor_gain1.0000
8:93772588:GGGC:Gacceptor_gain1.0000
8:93772588:GGGCA:Gacceptor_gain1.0000
8:93772647:GTTGG:Gdonor_gain1.0000
8:93772648:TTGG:Tdonor_gain1.0000
8:93772648:TTGGG:Tdonor_loss1.0000
8:93772650:GG:Gdonor_gain1.0000
8:93772651:GG:Gdonor_gain1.0000
8:93772651:GGT:Gdonor_loss1.0000
8:93772652:G:GCdonor_loss1.0000
8:93772652:G:GGdonor_gain1.0000
8:93772653:TAAG:Tdonor_loss1.0000
8:93781652:A:AGacceptor_gain1.0000
8:93781653:A:Gacceptor_gain1.0000

AlphaMissense

6566 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:93797376:G:CR669T0.999
8:93797399:T:AW677R0.999
8:93797399:T:CW677R0.999
8:93797366:A:CS666R0.998
8:93797368:C:AS666R0.998
8:93797368:C:GS666R0.998
8:93797372:T:AW668R0.998
8:93797372:T:CW668R0.998
8:93797376:G:TR669I0.998
8:93797377:A:CR669S0.998
8:93797377:A:TR669S0.998
8:93804765:T:CS776P0.998
8:93804796:G:AG786E0.998
8:93804811:G:AG791D0.998
8:93797194:T:AW641R0.997
8:93797194:T:CW641R0.997
8:93797390:G:CA674P0.997
8:93803672:C:GC770W0.997
8:93803679:A:CS773R0.997
8:93803681:T:AS773R0.997
8:93803681:T:GS773R0.997
8:93809872:A:CS917R0.997
8:93809874:C:AS917R0.997
8:93809874:C:GS917R0.997
8:93797196:G:CW641C0.996
8:93797196:G:TW641C0.996
8:93803670:T:CC770R0.996
8:93804865:T:CL809P0.996
8:93797191:G:CD640H0.995
8:93804795:G:AG786R0.995

dbSNP variants (sampled 300 via entrez): RS1000122389 (8:93784339 C>T), RS1000224211 (8:93826376 G>A,T), RS1000261528 (8:93790499 C>T), RS1000262173 (8:93784532 T>C), RS1000280591 (8:93778027 C>A,G,T), RS1000364618 (8:93754576 G>C), RS1000399542 (8:93773359 G>T), RS1000408789 (8:93830037 A>G), RS1000430654 (8:93773143 A>C), RS1000470544 (8:93826552 G>A,C), RS1000470934 (8:93756947 G>A), RS1000553877 (8:93811598 A>G), RS1000581019 (8:93802581 T>G), RS1000609951 (8:93778223 C>T), RS1000649347 (8:93804374 G>A,T)

Disease associations

OMIM: gene MIM:609884 | disease phenotypes: MIM:602152, MIM:607361, MIM:610688, MIM:613550, MIM:615991, MIM:213300, MIM:249000, MIM:216360, MIM:108600, MIM:256100, MIM:209900

GenCC curated gene-disease

DiseaseClassificationInheritance
COACH syndrome 1DefinitiveAutosomal recessive
Meckel syndrome, type 3DefinitiveAutosomal recessive
nephronophthisis 11DefinitiveAutosomal recessive
Joubert syndrome 6StrongAutosomal recessive
ciliopathyStrongAutosomal recessive
Joubert syndromeSupportiveAutosomal recessive
Meckel syndromeSupportiveAutosomal recessive
Senior-Boichis syndromeSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
ciliopathyDefinitiveAR

Mondo (29): RHYNS syndrome (MONDO:0011202), Meckel syndrome, type 3 (MONDO:0011821), Joubert syndrome 6 (MONDO:0012539), nephronophthisis 11 (MONDO:0013302), Bardet-Biedl syndrome 14 (MONDO:0014442), Joubert syndrome (MONDO:0018772), Meckel syndrome (MONDO:0018921), COACH syndrome 1 (MONDO:0800103), spastic ataxia (MONDO:0017845), Joubert syndrome and related disorders (MONDO:0015369), kidney disorder (MONDO:0005240), nephronophthisis (MONDO:0019005), coloboma (MONDO:0001476), cystic kidney disease (MONDO:0002473), pathologic nystagmus (MONDO:0004843)

Orphanet (15): Bardet-Biedl syndrome (Orphanet:110), RHYNS syndrome (Orphanet:140976), Joubert syndrome with hepatic defect (Orphanet:1454), Isolated Joubert syndrome (Orphanet:475), Meckel syndrome (Orphanet:564), Senior-Boichis syndrome (Orphanet:84081), Spastic ataxia (Orphanet:316226), Joubert syndrome and related disorders (Orphanet:140874), Nephronophthisis (Orphanet:655), Cerebellar malformation (Orphanet:182061), OBSOLETE: Ocular coloboma (Orphanet:194), Atypical hemolytic uremic syndrome (Orphanet:2134), Ciliopathy (Orphanet:363250), Coloboma of iris (Orphanet:98944), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

193 total (30 of 193 shown, HPO-id order):

HPOTerm
HP:0000002Abnormality of body height
HP:0000003Multicystic kidney dysplasia
HP:0000007Autosomal recessive inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000037Male pseudohermaphroditism
HP:0000062Ambiguous genitalia
HP:0000068Urethral atresia
HP:0000073Ureteral duplication
HP:0000083Renal insufficiency
HP:0000089Renal hypoplasia
HP:0000090Nephronophthisis
HP:0000092Renal tubular atrophy
HP:0000103Polyuria
HP:0000107Renal cyst
HP:0000108Renal corticomedullary cysts
HP:0000112Nephropathy
HP:0000122Unilateral renal agenesis
HP:0000154Wide mouth
HP:0000175Cleft palate
HP:0000202Orofacial cleft
HP:0000221Furrowed tongue
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000256Macrocephaly
HP:0000276Long face
HP:0000293Full cheeks
HP:0000311Round face
HP:0000316Hypertelorism
HP:0000340Sloping forehead

GWAS associations

0 associations (top):

MeSH disease descriptors (17)

DescriptorNameTree numbers
D065766Atypical Hemolytic Uremic SyndromeC12.050.351.968.419.936.463.500; C12.200.777.419.936.463.500; C12.950.419.936.463.500; C15.378.050.141.610.500; C15.378.140.855.925.500.500; C15.378.243.937.925.500.500
D020788Bardet-Biedl SyndromeC10.228.140.617.200; C11.270.684.624; C16.131.077.245.125; C16.320.184.125
D003103ColobomaC11.250.110; C11.270.147; C16.131.384.282
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D007674Kidney DiseasesC12.050.351.968.419; C12.200.777.419; C12.950.419
D052177Kidney Diseases, CysticC12.050.351.968.419.403; C12.200.777.419.403; C12.950.419.403
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
D009759Nystagmus, PathologicC10.292.562.675; C11.590.400
D016104OligohydramniosC12.050.703.560
D010195PancreatitisC06.689.750
D010538PeritonitisC01.463.600; C06.844.640
D051437Renal InsufficiencyC12.050.351.968.419.780; C12.200.777.419.780; C12.950.419.780
C567141Bardet-Biedl Syndrome 14 (supp.)
C537689Joubert syndrome 6 (supp.)
C536132Meckel syndrome type 3 (supp.)
C537612RHYNS syndrome (supp.)
C564815Spastic Ataxia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression2
Tobacco Smoke Pollutiondecreases expression2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression, increases methylation1
tris(2-butoxyethyl) phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
zinc chromatedecreases expression, increases abundance1
ochratoxin Adecreases acetylation1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
avobenzonedecreases expression1
chromium hexavalent iondecreases expression, increases abundance1
CGP 52608affects binding, increases reaction1
ICG 001decreases expression1
eprenetapoptaffects expression, affects reaction1
Sunitinibdecreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Cadmiumincreases abundance, increases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Methyl Methanesulfonateincreases expression1
Quercetindecreases expression1
Smokeincreases abundance, increases expression1
Thiramdecreases expression1
Tretinoindecreases expression1
Cyclosporineincreases expression1
Aflatoxin M1decreases expression1

Cellosaurus cell lines

1 cell lines: 1 finite cell line

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

CellosaurusNameCategorySex
CVCL_C7LKGM27987Finite cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00067990PHASE4COMPLETEDAngiotensin II Blockade for Chronic Allograft Nephropathy
NCT00117078PHASE4COMPLETEDAranesp® Monthly Preference Study - 2
NCT00117130PHASE4COMPLETEDStudy to Evaluate Effectiveness of Aranesp®
NCT00132431PHASE4COMPLETEDSTART: Sensipar Treatment Algorithm to Reach K/DOQI Targets in Chronic Kidney Disease Subjects With Secondary Hyperparathyroidism
NCT00140985PHASE4COMPLETEDAntiproteinuric Efficacy of Losartan Potassium in Patients With Non-Diabetic Proteinuric Renal Diseases (0954-213)
NCT00246129PHASE4COMPLETEDCamTac Trial:Campath-Tacrolimus vs IL2R MoAb/Tacrolimus/MMF in Renal Transplantation
NCT00275535PHASE4COMPLETEDThe Comparison of Tacrolimus and Sirolimus Immunosuppression Based Drug Regimens in Kidney Transplant Recipients
NCT00282217PHASE4COMPLETEDStudy Evaluating Sirolimus in the Treatment of Kidney Transplant
NCT00289614PHASE4COMPLETEDPatients With Renal Impairment and Diabetes Undergoing Computed Tomography (CT)
NCT00290069PHASE4UNKNOWNRenal Function Optimization With Mycophenolate Mofetil (MMF) Immunosuppressor Regimes (ALHAMBRA)
NCT00338468PHASE4TERMINATEDA Study to Assess Disability in Anemic Elderly Patients With Kidney Disease Receiving PROCRIT (Epoetin Alfa)
NCT00368901PHASE4COMPLETEDSTAAR-2 Clinical Study
NCT00369733PHASE4COMPLETEDSTAAR-3 Clinical Study
NCT00369772PHASE4COMPLETEDSTAAR-1 Clinical Study
NCT00379899PHASE4COMPLETEDADVANCE: Study to Evaluate Cinacalcet Plus Low Dose Vitamin D on Vascular Calcification in Subjects With Chronic Kidney Disease Receiving Hemodialysis
NCT00443508PHASE4UNKNOWNReduction or Discontinuation of CNI’s With Conversion to Everolimus-Based Immunosuppresion
NCT00452478PHASE4TERMINATEDConversion From Standard Phosphate Binder Therapy to Fosrenol® (Lanthanum Carbonate) in Chronic Kidney Disease Stage 5
NCT00492518PHASE4COMPLETEDAcetylcysteine, Theophylline, and a Combination of Both in the Prophylaxis of Contrast-Induced Nephropathy
NCT00505102PHASE4UNKNOWNSafe Renal Function In Long Term Heart Transplanted Patients
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00688480PHASE4COMPLETEDDo Xanthine Oxidase Inhibitors Reduce Both Left Ventricular Hypertrophy and Endothelial Dysfunction in Cardiovascular Patients With Renal Dysfunction?
NCT00863707PHASE4COMPLETEDA Study of the Safety and Tolerance of Regadenoson in Subjects With Renal Impairment
NCT01101698PHASE4UNKNOWNVitamin K2 and Vessel Calcification in Chronic Kidney Disease Patients
NCT01150201PHASE4COMPLETEDAliskiren Combined With Losartan in Proteinuric, Non-diabetic Chronic Kidney Disease
NCT01155141PHASE4COMPLETEDIdiopathic Focal Segmental Glomerulosclerosis (FSGS) and Treatment With ACTH
NCT01228279PHASE4COMPLETEDSympathetic Activity in Patients With End-stage Renal Disease on Peritoneal Dialysis
NCT01334333PHASE4COMPLETEDComparison of Medication Adherence Between Once and Twice Daily Tacrolimus in Stable Renal Transplant Recipients
NCT01437943PHASE4TERMINATEDEffect of Short Term Aliskiren Treatment in Kidney Transplant Patients
NCT01545479PHASE4COMPLETEDIncreased Renal Oxygenation and Angiotensin Converting Enzyme Inhibition
NCT01614431PHASE4COMPLETEDN Acetyl Cysteine for Cystinosis Patients
NCT01631149PHASE4COMPLETEDEffect of Deep BLock on Intraoperative Surgical Conditions
NCT01722513PHASE4UNKNOWNEfficacy and Safety of Alprostadil Prevent Contrast Induced Nephropathy
NCT01985360PHASE4COMPLETEDISCHEMIA-Chronic Kidney Disease Trial
NCT02311010PHASE4UNKNOWNPractical Use of Advagraf de Novo After Kidney Transplantation According to Recipient Genetic Polymorphism
NCT02413073PHASE4COMPLETEDWhole Body Vibration in Kidney Disease
NCT02444013PHASE4UNKNOWNFolic Acid for Prevention of Contrast Induced Nephropathy
NCT02663713PHASE4COMPLETEDA Randomized, Pharmacodynamic Comparison of Low Dose Ticagrelor to Clopidogrel in Patients With Prior Myocardial Infarction
NCT02707809PHASE4COMPLETEDEffects of Dexmedetomidine on Microcirculation of Kidney Transplant Recipient
NCT02761577PHASE4COMPLETEDA Prospective Study on Incidence and Prevention of Contrast-induced Nephropathy in Croatia
NCT03029351PHASE4TERMINATEDGLP-1 Receptor Agonist Therapy and Albuminuria in Patients With Type 2 Diabetes