TMEM254

protein-coding

transmembrane protein 254

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf57

MANE transcript

NM_025125.4

Inheritance

—

ClinVar variants

U:23B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr10:80,078,646-80,092,557

External References & Databases

Ensembl (ENSG00000133678)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 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 TMEM254 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025125.4. 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				1 clinvar		1
missense			23 clinvar	2 clinvar		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	3	0	26

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025125.4	RefSeq	NP_079401.2	4	MANE Select
ENST00000372281.8	Ensembl	ENSP00000361355.3	4	MANE Select
NM_001270367.1	RefSeq	NP_001257296.1	4	Standard
NM_001270368.1	RefSeq	NP_001257297.1	3	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: ENST00000372281
Coding exons: 4
Length: 13912
Individuals with no LoFs: 125660
Homozygous LoFs: 0
Heterozygous LoFs: 87
Defined: 125747
p: 0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.319	75	67.6	1.11	0.00000348	784
Missense (PolyPhen)		25	17.57	1.4229		239
Synonymous	0.825	20	25.3	0.791	0.00000120	236
Loss of Function	0.690	5	6.97	0.718	2.97e-7	74

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00019	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.0027	0.0025	notable
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

RVIS EVS: -0.16
RVIS percentile EVS: 41.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N