FAM25A

family with sequence similarity 25 member A

Basic information

Region (hg38): 10:87020294-87024730

Links

ENSG00000188100 ∙ NCBI:643161 ∙ ∙ HGNC:23436 ∙ Uniprot:B3EWG3 ∙ 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 FAM25A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM25A 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in FAM25A

This is a list of pathogenic ClinVar variants found in the FAM25A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-87020370-C-T		not specified	Uncertain significance (Jun 11, 2021)
10-87020371-G-A		not specified	Uncertain significance (Jul 01, 2024)
10-87022322-G-A		not specified	Uncertain significance (Oct 27, 2022)
10-87022328-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-87022341-A-G		not specified	Uncertain significance (Dec 10, 2024)
10-87022355-G-A		not specified	Uncertain significance (Feb 07, 2025)
10-87024555-A-G		not specified	Uncertain significance (Jan 04, 2022)
10-87024556-T-G		not specified	Uncertain significance (Oct 03, 2022)
10-87024588-A-T		not specified	Uncertain significance (Jan 02, 2025)
10-87024600-A-G		not specified	Uncertain significance (May 03, 2023)
10-87024639-C-T		not specified	Uncertain significance (Jun 30, 2023)
10-87024651-A-G		not specified	Likely benign (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM25A	protein_coding	protein_coding	ENST00000343959	3	4425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.199	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.698	35	48.7	0.719	0.00000246	560
Missense in Polyphen
Synonymous	0.579	17	20.3	0.837	0.00000121	177
Loss of Function	0.980	1	2.75	0.363	1.15e-7	37

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

Haploinsufficiency Scores

• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.340

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam25c