TMC2

transmembrane channel like 2, the group of Transmembrane channel like family

Basic information

Region (hg38): 20:2536572-2643580

Previous symbols: [ "C20orf145" ]

Links

ENSG00000149488 ∙ NCBI:117532 ∙ OMIM:606707 ∙ HGNC:16527 ∙ Uniprot:Q8TDI7 ∙ 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 TMC2 gene.

• Inborn genetic diseases (38 variants)
• not provided (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMC2 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				2	1	3
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					23	23
Total	0	0	37	3	24

Variants in TMC2

This is a list of pathogenic ClinVar variants found in the TMC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-2537290-G-A		not specified	Uncertain significance (Jun 13, 2022)
20-2558472-G-C		not specified	Uncertain significance (Sep 27, 2022)
20-2558554-G-A		not specified	Uncertain significance (Jun 09, 2022)
20-2558633-A-G		not specified	Uncertain significance (Mar 24, 2023)
20-2558641-G-A		not specified	Likely benign (Oct 14, 2021)
20-2561952-C-T		not specified	Uncertain significance (Jun 24, 2022)
20-2561967-C-T		not specified	Uncertain significance (Jun 11, 2021)
20-2562023-C-T			Benign (Nov 12, 2018)
20-2572171-C-T			Likely benign (Oct 13, 2017)
20-2572191-A-T		not specified	Uncertain significance (Dec 28, 2023)
20-2572223-A-C		not specified	Uncertain significance (Nov 22, 2022)
20-2572240-C-G		not specified	Uncertain significance (Jun 23, 2023)
20-2579132-G-C			Benign (Jun 19, 2021)
20-2579147-A-G		not specified	Uncertain significance (Dec 12, 2023)
20-2579974-C-T		not specified	Uncertain significance (Sep 09, 2021)
20-2580049-T-C		not specified	Uncertain significance (Feb 15, 2023)
20-2592170-T-G			Benign (Jun 19, 2021)
20-2592406-G-C		not specified	Uncertain significance (Feb 23, 2023)
20-2594831-A-G		not specified	Uncertain significance (Apr 06, 2022)
20-2594843-G-C		not specified	Uncertain significance (Oct 05, 2021)
20-2594853-A-G		not specified	Uncertain significance (Nov 17, 2022)
20-2594898-G-A		not specified	Uncertain significance (Apr 10, 2023)
20-2594927-G-T		not specified	Uncertain significance (Feb 06, 2024)
20-2597182-G-A		not specified	Uncertain significance (Jul 15, 2021)
20-2597192-G-A		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMC2	protein_coding	protein_coding	ENST00000358864	20	105178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.08e-27	0.00126	124688	5	1055	125748	0.00422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.226	492	506	0.972	0.0000272	5915
Missense in Polyphen		213	197.31	1.0795		2284
Synonymous	0.742	184	197	0.933	0.0000109	1756
Loss of Function	0.679	44	49.1	0.895	0.00000277	534

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00582	0.00583
Ashkenazi Jewish	0.00220	0.00218
East Asian	0.000381	0.000381
Finnish	0.000971	0.000971
European (Non-Finnish)	0.00721	0.00714
Middle Eastern	0.000381	0.000381
South Asian	0.00102	0.000980
Other	0.00408	0.00408

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ion channel required for the normal function of cochlear hair cells (PubMed:11850618). Component of the hair cell's mechanotransduction (MET) machinery. Involved in mechanosensitive responses of the hair cells (By similarity). {ECO:0000250|UniProtKB:E7FFT2, ECO:0000269|PubMed:11850618}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.68

Haploinsufficiency Scores

• pHI: 0.0561
• hipred: N
• hipred_score: 0.275
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmc2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: detection of mechanical stimulus involved in sensory perception of sound;vestibular reflex;calcium ion transmembrane transport;regulation of calcium ion transmembrane transport
• Cellular component: cellular_component;integral component of plasma membrane;stereocilium tip
• Molecular function: molecular_function;ion channel activity;voltage-gated calcium channel activity;mechanosensitive ion channel activity