TMEM253

transmembrane protein 253

Basic information

Region (hg38): 14:21098811-21103724

Previous symbols: [ "NCRNA00220", "C14orf95", "C14orf176" ]

Links

ENSG00000232070 ∙ NCBI:643382 ∙ ∙ HGNC:32545 ∙ Uniprot:P0C7T8 ∙ 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 TMEM253 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM253 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in TMEM253

This is a list of pathogenic ClinVar variants found in the TMEM253 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-21101351-A-G		not specified	Uncertain significance (May 11, 2022)
14-21101368-G-C		not specified	Uncertain significance (Feb 08, 2025)
14-21101389-C-T		not specified	Uncertain significance (Apr 13, 2023)
14-21101398-A-G		not specified	Uncertain significance (Aug 28, 2023)
14-21101416-A-T		not specified	Uncertain significance (Nov 24, 2024)
14-21101895-G-A		not specified	Uncertain significance (Oct 12, 2021)
14-21101950-C-A		not specified	Uncertain significance (Sep 30, 2024)
14-21101962-G-T		not specified	Uncertain significance (Dec 18, 2023)
14-21102082-G-A		not specified	Uncertain significance (Jun 21, 2022)
14-21102097-C-T		not specified	Uncertain significance (Jan 01, 2025)
14-21102409-G-A		not specified	Likely benign (Jun 03, 2022)
14-21102421-T-C		not specified	Uncertain significance (Aug 14, 2024)
14-21102429-A-T		not specified	Uncertain significance (Oct 18, 2021)
14-21102446-G-T		not specified	Uncertain significance (Feb 17, 2022)
14-21102468-G-A		not specified	Uncertain significance (Dec 12, 2023)
14-21102501-A-G		not specified	Uncertain significance (Dec 14, 2021)
14-21102635-T-A		not specified	Uncertain significance (Jun 27, 2023)
14-21102675-A-T		not specified	Uncertain significance (Nov 02, 2023)
14-21102702-C-T		not specified	Likely benign (Jul 06, 2021)
14-21102705-G-A		not specified	Uncertain significance (Jul 14, 2024)
14-21102729-A-G		not specified	Uncertain significance (May 31, 2023)
14-21103196-A-C		not specified	Uncertain significance (May 09, 2022)
14-21103208-G-A		not specified	Uncertain significance (Mar 12, 2024)
14-21103218-G-A		not specified	Uncertain significance (Jul 06, 2021)
14-21103220-C-G		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM253	protein_coding	protein_coding	ENST00000418511	6	4788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000139	0.229	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.593	100	118	0.847	0.00000595	1367
Missense in Polyphen		35	37.885	0.92384		441
Synonymous	1.05	37	46.0	0.804	0.00000227	462
Loss of Function	0.0355	9	9.12	0.987	3.86e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem253

Gene ontology

• Cellular component: integral component of membrane