TMEM254

transmembrane protein 254

Basic information

Region (hg38): 10:80078646-80092557

Previous symbols: [ "C10orf57" ]

Links

ENSG00000133678 ∙ NCBI:80195 ∙ ∙ HGNC:25804 ∙ Uniprot:Q8TBM7 ∙ 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 TMEM254 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM254 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in TMEM254

This is a list of pathogenic ClinVar variants found in the TMEM254 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80078748-T-C		not specified	Uncertain significance (Sep 16, 2021)
10-80090805-G-A		not specified	Uncertain significance (Jun 19, 2024)
10-80090820-G-A		not specified	Likely benign (Sep 27, 2021)
10-80090832-T-A		not specified	Uncertain significance (Dec 16, 2022)
10-80090841-T-A		not specified	Uncertain significance (Dec 27, 2023)
10-80090851-C-A		not specified	Uncertain significance (Apr 06, 2024)
10-80090864-G-A		not specified	Uncertain significance (May 03, 2023)
10-80090878-C-G		not specified	Uncertain significance (Nov 15, 2021)
10-80090894-C-T		not specified	Uncertain significance (Dec 19, 2023)
10-80090895-G-A		not specified	Likely benign (Sep 17, 2021)
10-80090895-G-T		not specified	Uncertain significance (Oct 18, 2021)
10-80090900-C-T		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM254	protein_coding	protein_coding	ENST00000372281	4	13912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00133	0.670	125660	0	87	125747	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.319	75	67.6	1.11	0.00000348	784
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000186
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00266	0.00245
Other	0.000355	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tmem254c

Gene ontology

• Cellular component: integral component of membrane