TMCO5A

transmembrane and coiled-coil domains 5A

Basic information

Region (hg38): 15:37921939-37967724

Previous symbols: [ "TMCO5" ]

Links

ENSG00000166069 ∙ NCBI:145942 ∙ ∙ HGNC:28558 ∙ Uniprot:Q8N6Q1 ∙ 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 TMCO5A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCO5A 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in TMCO5A

This is a list of pathogenic ClinVar variants found in the TMCO5A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-37936327-G-A		not specified	Uncertain significance (Mar 13, 2023)
15-37936872-C-T		not specified	Uncertain significance (May 05, 2023)
15-37936927-G-T		not specified	Uncertain significance (Mar 17, 2023)
15-37937362-C-T		not specified	Uncertain significance (Jul 14, 2021)
15-37938158-C-A		not specified	Uncertain significance (Apr 07, 2023)
15-37941161-C-A		not specified	Uncertain significance (Jun 21, 2022)
15-37941170-G-A		not specified	Uncertain significance (Aug 01, 2022)
15-37941177-A-C		not specified	Uncertain significance (Feb 28, 2023)
15-37941692-G-C		not specified	Uncertain significance (Nov 21, 2023)
15-37941693-T-G		not specified	Uncertain significance (Dec 18, 2023)
15-37942204-C-T		not specified	Uncertain significance (Dec 27, 2022)
15-37942233-G-T		not specified	Uncertain significance (Dec 15, 2022)
15-37947659-A-T		not specified	Uncertain significance (Jan 04, 2022)
15-37947665-A-C		not specified	Uncertain significance (Jan 23, 2024)
15-37947673-G-C		Malignant tumor of prostate	Uncertain significance (-)
15-37951157-A-G		not specified	Uncertain significance (Oct 27, 2021)
15-37951173-A-G		not specified	Uncertain significance (Feb 22, 2023)
15-37951188-T-C		not specified	Uncertain significance (May 16, 2023)
15-37951230-A-G		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCO5A	protein_coding	protein_coding	ENST00000319669	10	45786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000449	0.855	125612	0	56	125668	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0225	143	144	0.995	0.00000701	1906
Missense in Polyphen		42	42.188	0.99554		651
Synonymous	-1.41	67	53.9	1.24	0.00000287	482
Loss of Function	1.45	11	17.5	0.627	7.41e-7	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000462	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.000762	0.000762
Finnish	0.00	0.00
European (Non-Finnish)	0.000249	0.000246
Middle Eastern	0.000762	0.000762
South Asian	0.000164	0.000163
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0573

Intolerance Scores

• loftool: 0.332
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

• pHI: 0.0560
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 1.14e-7

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmco5
• Phenotype: normal phenotype

Gene ontology

• Cellular component: integral component of membrane