TMC4

transmembrane channel like 4, the group of Transmembrane channel like family

Basic information

Region (hg38): 19:54160107-54173250

Links

ENSG00000167608 ∙ NCBI:147798 ∙ OMIM:617181 ∙ HGNC:22998 ∙ Uniprot:Q7Z404 ∙ 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 TMC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMC4 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		2
missense			26	6		32
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	9	0

Variants in TMC4

This is a list of pathogenic ClinVar variants found in the TMC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54160315-C-T		TMC4-related disorder	Likely benign (Dec 08, 2023)
19-54160516-G-A		not specified	Uncertain significance (Nov 03, 2022)
19-54160909-C-T		TMC4-related disorder	Likely benign (May 04, 2023)
19-54160912-G-C		not specified	Uncertain significance (Feb 06, 2023)
19-54160941-G-A		not specified	Uncertain significance (Apr 15, 2024)
19-54161163-A-C		not specified	Uncertain significance (Apr 19, 2024)
19-54161205-G-A		not specified	Likely benign (Jul 06, 2021)
19-54162256-A-G		not specified	Uncertain significance (Feb 06, 2024)
19-54162275-C-T		not specified	Uncertain significance (Jan 31, 2023)
19-54162748-T-A		not specified	Uncertain significance (Nov 08, 2022)
19-54163088-C-T		not specified	Uncertain significance (May 04, 2022)
19-54163825-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-54163851-G-T		not specified	Uncertain significance (Sep 26, 2022)
19-54164460-C-T		not specified	Uncertain significance (May 28, 2024)
19-54164468-A-T		not specified	Uncertain significance (May 04, 2022)
19-54164496-C-T		not specified	Uncertain significance (Oct 10, 2023)
19-54164541-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-54164579-A-G		not specified	Uncertain significance (Sep 22, 2023)
19-54165436-T-C		not specified	Uncertain significance (Jan 29, 2024)
19-54165453-C-T		not specified	Uncertain significance (Feb 17, 2024)
19-54165526-C-T		not specified	Uncertain significance (Jul 11, 2023)
19-54165564-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-54168195-A-G		not specified	Uncertain significance (Apr 18, 2023)
19-54168240-C-T		not specified	Likely benign (Jan 26, 2023)
19-54168246-C-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMC4	protein_coding	protein_coding	ENST00000376591	15	13099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-13	0.559	125592	0	156	125748	0.000620

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	346	407	0.851	0.0000238	4437
Missense in Polyphen		96	122.03	0.78669		1381
Synonymous	0.483	175	183	0.955	0.0000108	1569
Loss of Function	1.53	25	34.8	0.719	0.00000174	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000831	0.000819
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000599	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000782	0.000756
Middle Eastern	0.000599	0.000544
South Asian	0.00128	0.00127
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0868

Intolerance Scores

• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.68

Haploinsufficiency Scores

• pHI: 0.0233
• hipred: N
• hipred_score: 0.238
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmc4

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