TMCO5A

protein-coding

transmembrane and coiled-coil domains 5A

Gene summary

Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

TMCO5

MANE transcript

NM_152453.4

Inheritance

—

ClinVar variants

U:46B:3

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr15:37,921,939-37,967,724

External References & Databases

Ensembl (ENSG00000166069)

Transcript & Mutation Effects

hg38 • Region Span ~45.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMCO5A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152453.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			46 clinvar	3 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	3	0	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152453.4	RefSeq	NP_689666.2	10	MANE Select
ENST00000319669.5	Ensembl	ENSP00000327234.4	10	MANE Select
NM_001330255.2	RefSeq	NP_001317184.1	10	Standard
NM_001370735.1	RefSeq	NP_001357664.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319669
Coding exons: 10
Length: 45786
Individuals with no LoFs: 125612
Homozygous LoFs: 0
Heterozygous LoFs: 56
Defined: 125668
p: 0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0225	143	144	0.995	0.00000701	1906
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00076	0.00076	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00016	0.00016	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0573

Intolerance Scores

LoFtool: 0.332
RVIS EVS: 0.68
RVIS percentile EVS: 85.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 1.14e-7

Gene Damage Prediction

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