TMEM47

Chr X

transmembrane protein 47

Also known as: BCMP1, TM4SF10, VAB-9

NCBI Gene: 83604ENSG00000147027UniProt: Q9BQJ4OMIM: 300698

The protein regulates cell junction organization in epithelial cells and controls the transition from adherens junctions to tight junctions, while also regulating F-actin polymerization and affecting junctional protein localization. TMEM47 is highly constrained against loss-of-function variants (pLI 0.80, LOEUF 0.57), but no established human disease associations have been reported to date. Further research is needed to determine if mutations in this gene cause developmental or neurological disorders.

OMIMResearchSummary from RefSeq, UniProt
GOFmechanismLOEUF 0.57
Clinical Summary— TMEM47
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.80) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
71 unique Pathogenic / Likely Pathogenic· 11 VUS of 100 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.57LOEUF
pLI 0.797
Z-score 2.13
OE 0.00 (0.00–0.57)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.01Z-score
OE missense 0.64 (0.50–0.84)
41 obs / 63.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–0.57)
0≤0.351.4
Missense OE0.64 (0.50–0.84)
0≤0.61.4
Synonymous OE1.30
0≤1.21.6
LoF obs/exp: 0 / 5.3Missense obs/exp: 41 / 63.7Syn Z: -1.23
DN
0.3594th %ile
GOF
0.6443th %ile
LOF
0.51top 25%

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

100 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic69
Likely Pathogenic2
VUS11
Likely Benign4
69
Pathogenic
2
Likely Pathogenic
11
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
69
0
69
Likely Pathogenic
0
0
2
0
2
VUS
0
8
3
0
11
Likely Benign
0
0
2
2
4
Benign
0
0
0
0
0
Total0876286

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

TMEM47 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Prognostic implications and therapeutic opportunities related to CAF subtypes in CMS4 colorectal cancer: insights from single-cell and bulk transcriptomics.
Ma M et al.·Apoptosis
2025
Integration of scRNA and bulk RNA-sequence to construct the 5-gene molecular prognostic model based on the heterogeneity of thyroid carcinoma endothelial cell
Ni Z et al.·Acta Biochim Biophys Sin (Shanghai)
2024Functional
Four functional genotoxic marker genes (Bax, Btg2, Ccng1, and Cdkn1a) discriminate genotoxic hepatocarcinogens from non-genotoxic hepatocarcinogens and non-genotoxic non-hepatocarcinogens in rat public toxicogenomics data, Open TG-GATEs
Furihata C et al.·Genes Environ
2024Functional
Implication of genetic variants in primary microRNA processing sites in the risk of multiple sclerosis
Hecker M et al.·EBioMedicine
2022
Identification of potential novel biomarkers for abdominal aortic aneurysm based on comprehensive analysis of circRNA-miRNA-mRNA networks
Li T et al.·Exp Ther Med
2021
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Improving Risk Stratification for Pediatric Patients with Rhabdomyosarcoma by Molecular Detection of Disseminated Disease.
Lak NSM et al.·Clin Cancer Res
2021Cohort
Organ-specific adaptive signaling pathway activation in metastatic breast cancer cells.
Burnett RM et al.·Oncotarget
2015
Application of a co‑expression network for the analysis of aggressive and non‑aggressive breast cancer cell lines to predict the clinical outcome of patients.
Guo L et al.·Mol Med Rep
2017Cohort
[Diagnosis of a patient with adjacent gene deletion syndrome with DMD complete deletion type of Duchenne muscular dystrophy].
Liu L et al.·Zhonghua Yi Xue Yi Chuan Xue Za Zhi
2021Case report
Clinical significance and functional role of transmembrane protein 47 (TMEM47) in chemoresistance of hepatocellular carcinoma.
Ng KT et al.·Int J Oncol
2020Functional
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients