TMC3

transmembrane channel like 3, the group of Transmembrane channel like family

Basic information

Region (hg38): 15:81331088-81374213

Links

ENSG00000188869 ∙ NCBI:342125 ∙ OMIM:617196 ∙ HGNC:22995 ∙ Uniprot:Q7Z5M5 ∙ 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 TMC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMC3 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				1		1
missense			60	5		65
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	6	1

Variants in TMC3

This is a list of pathogenic ClinVar variants found in the TMC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-81332430-A-T		not specified	Uncertain significance (Aug 09, 2021)
15-81332437-C-G		not specified	Uncertain significance (Feb 23, 2023)
15-81332553-C-T		not specified	Likely benign (Apr 20, 2024)
15-81332560-G-T		not specified	Uncertain significance (Dec 03, 2021)
15-81332577-T-C		not specified	Uncertain significance (Sep 26, 2023)
15-81332588-G-T		not specified	Benign (Nov 06, 2015)
15-81332606-G-A			Likely benign (Jun 01, 2022)
15-81332620-G-T		not specified	Uncertain significance (Jan 04, 2024)
15-81332640-G-A		not specified	Uncertain significance (Aug 12, 2022)
15-81332661-A-G		not specified	Uncertain significance (Jul 06, 2022)
15-81332775-G-C		not specified	Uncertain significance (Jan 10, 2023)
15-81332790-A-T		not specified	Uncertain significance (Mar 18, 2024)
15-81332794-C-G		not specified	Uncertain significance (Jan 26, 2022)
15-81332798-C-T		not specified	Uncertain significance (May 11, 2022)
15-81332801-A-G		not specified	Uncertain significance (May 23, 2023)
15-81332819-C-T		not specified	Uncertain significance (Sep 14, 2022)
15-81332858-T-C		not specified	Uncertain significance (Dec 26, 2023)
15-81332925-G-C		not specified	Uncertain significance (Mar 30, 2024)
15-81332949-C-T		not specified	Likely benign (Feb 15, 2023)
15-81332950-G-C		not specified	Uncertain significance (Feb 04, 2022)
15-81333081-T-A		not specified	Uncertain significance (Mar 15, 2024)
15-81333093-C-T		not specified	Likely benign (Feb 15, 2023)
15-81333101-G-A		not specified	Uncertain significance (Jun 28, 2023)
15-81333114-G-T		not specified	Uncertain significance (Nov 15, 2021)
15-81333131-T-C		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMC3	protein_coding	protein_coding	ENST00000359440	22	42997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.89e-22	0.0595	124497	1	161	124659	0.000650

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.514	582	618	0.942	0.0000347	7196
Missense in Polyphen		137	158.04	0.86686		1958
Synonymous	0.335	237	244	0.973	0.0000148	2100
Loss of Function	1.35	39	49.2	0.792	0.00000259	543

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00122
Ashkenazi Jewish	0.00	0.00
East Asian	0.000502	0.000501
Finnish	0.00	0.00
European (Non-Finnish)	0.000908	0.000894
Middle Eastern	0.000502	0.000501
South Asian	0.000783	0.000719
Other	0.000846	0.000826

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.878
• rvis_EVS: 1.48
• rvis_percentile_EVS: 95.29

Haploinsufficiency Scores

• pHI: 0.0559
• hipred: N
• hipred_score: 0.289

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmc3

Gene ontology

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