FAM131A

family with sequence similarity 131 member A

Basic information

Region (hg38): 3:184335925-184348421

Previous symbols: [ "C3orf40" ]

Links

ENSG00000175182 ∙ NCBI:131408 ∙ ∙ HGNC:28308 ∙ Uniprot:Q6UXB0 ∙ 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 FAM131A gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM131A 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in FAM131A

This is a list of pathogenic ClinVar variants found in the FAM131A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-184338396-A-T		not specified	Uncertain significance (Jun 03, 2022)
3-184338418-G-T		not specified	Uncertain significance (Sep 16, 2021)
3-184341794-C-T		FAM131A-related disorder	Likely benign (Feb 21, 2022)
3-184342221-G-A		not specified	Uncertain significance (May 31, 2023)
3-184342224-G-A		not specified	Uncertain significance (May 27, 2022)
3-184342786-C-T		not specified	Uncertain significance (May 27, 2022)
3-184342849-G-T		not specified	Uncertain significance (May 04, 2022)
3-184344581-G-A		not specified	Uncertain significance (Jan 23, 2024)
3-184344596-G-A		not specified	Uncertain significance (Apr 22, 2022)
3-184344606-A-C		not specified	Uncertain significance (Aug 02, 2022)
3-184344693-T-G		not specified	Uncertain significance (Feb 10, 2022)
3-184344707-C-G		not specified	Uncertain significance (Jan 11, 2023)
3-184344734-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-184344776-G-T		not specified	Uncertain significance (Jul 06, 2021)
3-184344792-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-184344822-C-T		not specified	Uncertain significance (Dec 07, 2021)
3-184344868-A-C		FAM131A-related disorder	Likely benign (Aug 09, 2019)
3-184344876-C-T		not specified	Uncertain significance (Dec 14, 2022)
3-184344955-G-A		FAM131A-related disorder	Likely benign (Jun 03, 2019)
3-184346596-C-T		CLCN2-related disorder	Benign (Nov 05, 2019)
3-184346598-C-T		CLCN2-related disorder	Likely benign (Mar 27, 2019)
3-184346609-T-C			Likely benign (Dec 21, 2023)
3-184346612-G-A			Likely benign (Jan 01, 2023)
3-184346620-C-T		See cases • Inborn genetic diseases	Conflicting classifications of pathogenicity (Aug 17, 2023)
3-184346621-G-A			Likely benign (Jan 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM131A	protein_coding	protein_coding	ENST00000383847	6	10350

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00667	0.990	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	155	224	0.692	0.0000142	2312
Missense in Polyphen		81	103.23	0.78468		1045
Synonymous	0.375	95	99.8	0.952	0.00000644	801
Loss of Function	2.56	7	19.0	0.367	0.00000125	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000500	0.0000462
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000329	0.0000327
Other	0.000829	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0970

Intolerance Scores

• loftool: 0.529
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.380
• hipred: N
• hipred_score: 0.319
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam131a

Gene ontology

• Cellular component: extracellular region