TMC5

transmembrane channel like 5, the group of Transmembrane channel like family

Basic information

Region (hg38): 16:19410496-19499113

Links

ENSG00000103534 ∙ NCBI:79838 ∙ OMIM:617197 ∙ HGNC:22999 ∙ Uniprot:Q6UXY8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMC5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			52	5		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	5	0

Variants in TMC5

This is a list of pathogenic ClinVar variants found in the TMC5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-19440461-C-A		not specified	Likely benign (Jun 11, 2021)
16-19440706-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-19460266-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-19460310-C-T		not specified	Uncertain significance (Jul 13, 2021)
16-19460312-A-G		not specified	Uncertain significance (Feb 28, 2023)
16-19460325-G-A			Likely benign (Oct 01, 2022)
16-19463366-G-A		not specified	Likely benign (Mar 08, 2025)
16-19463783-G-A		not specified	Uncertain significance (Feb 12, 2025)
16-19463832-G-T		not specified	Uncertain significance (Sep 06, 2022)
16-19463840-C-T		not specified	Uncertain significance (Apr 22, 2022)
16-19463852-T-C		not specified	Uncertain significance (Oct 12, 2021)
16-19463875-G-A		not specified	Uncertain significance (Sep 29, 2023)
16-19463971-G-A		not specified	Uncertain significance (Apr 13, 2023)
16-19463982-G-C		not specified	Uncertain significance (Mar 11, 2022)
16-19466089-T-G		not specified	Uncertain significance (Sep 04, 2024)
16-19466101-T-C		not specified	Uncertain significance (May 23, 2023)
16-19466145-A-G		not specified	Uncertain significance (Sep 24, 2024)
16-19466151-G-A		not specified	Uncertain significance (Apr 07, 2022)
16-19466155-C-T		not specified	Uncertain significance (May 05, 2023)
16-19466193-G-A		not specified	Uncertain significance (Jan 16, 2024)
16-19469684-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-19469730-G-A		not specified	Likely benign (Dec 01, 2022)
16-19472133-A-G		not specified	Uncertain significance (Jan 10, 2023)
16-19472148-C-T		not specified	Uncertain significance (Dec 03, 2024)
16-19472163-A-G		not specified	Likely benign (Mar 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMC5	protein_coding	protein_coding	ENST00000396229	20	88618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.99e-8	1.00	125666	0	80	125746	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.653	503	546	0.921	0.0000288	6640
Missense in Polyphen		100	133.58	0.7486		1727
Synonymous	-0.754	219	205	1.07	0.0000112	1926
Loss of Function	3.81	21	50.1	0.419	0.00000247	591

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000542	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.000739	0.000739
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000327	0.000326
South Asian	0.000458	0.000457
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ion channel. {ECO:0000250}.

Recessive Scores

• pRec: 0.0860

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.29

Haploinsufficiency Scores

• pHI: 0.0815
• hipred: N
• hipred_score: 0.280
• ghis: 0.379

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0913

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmc5

Zebrafish Information Network

• Gene name: tmc5
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: ion transmembrane transport
• Cellular component: integral component of plasma membrane;extracellular exosome
• Molecular function: ion channel activity;mechanosensitive ion channel activity