TMEM25

transmembrane protein 25, the group of C2-set domain containing

Basic information

Region (hg38): 11:118531041-118547280

Links

ENSG00000149582 ∙ NCBI:84866 ∙ OMIM:613934 ∙ HGNC:25890 ∙ Uniprot:Q86YD3 ∙ 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 TMEM25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM25 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			40	1		41
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	1

Variants in TMEM25

This is a list of pathogenic ClinVar variants found in the TMEM25 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118532165-A-T		not specified	Uncertain significance (Nov 08, 2024)
11-118532224-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-118532242-G-C		not specified	Uncertain significance (Jun 27, 2022)
11-118532258-C-A		not specified	Uncertain significance (Oct 20, 2024)
11-118532274-G-C		not specified	Uncertain significance (Nov 21, 2023)
11-118532278-C-G		not specified	Uncertain significance (Jan 20, 2023)
11-118532354-G-T			Likely benign (Jul 01, 2022)
11-118532357-C-T		not specified	Uncertain significance (Jun 17, 2024)
11-118532377-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-118532396-A-G		not specified	Uncertain significance (Sep 26, 2024)
11-118532437-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-118532940-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-118532943-G-A		not specified	Uncertain significance (Jan 17, 2023)
11-118533001-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-118533001-G-T		not specified	Uncertain significance (Aug 03, 2022)
11-118533010-C-T		not specified	Uncertain significance (Feb 27, 2023)
11-118533019-A-G		not specified	Uncertain significance (Dec 14, 2023)
11-118533033-G-C		not specified	Uncertain significance (Dec 16, 2023)
11-118533054-G-T		not specified	Uncertain significance (Aug 05, 2024)
11-118533068-C-A		not specified	Uncertain significance (Jun 06, 2023)
11-118533075-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-118533085-C-A		not specified	Uncertain significance (Jun 26, 2023)
11-118533117-G-A		not specified	Uncertain significance (Mar 31, 2024)
11-118533129-C-T		not specified	Uncertain significance (Nov 18, 2022)
11-118533148-A-G		Autism	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM25	protein_coding	protein_coding	ENST00000313236	8	16240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-11	0.0407	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.311	215	228	0.942	0.0000141	2312
Missense in Polyphen		68	70.325	0.96695		799
Synonymous	0.408	95	100	0.948	0.00000612	827
Loss of Function	-0.112	16	15.5	1.03	7.47e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000506
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000707	0.000707
South Asian	0.000425	0.000425
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.940
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.282
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.680

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem25

Gene ontology

• Cellular component: extracellular region;plasma membrane;integral component of membrane
• Molecular function: protein binding