FAM3A

FAM3 metabolism regulating signaling molecule A

Basic information

Region (hg38): X:154506158-154516242

Links

ENSG00000071889 ∙ NCBI:60343 ∙ OMIM:300492 ∙ HGNC:13749 ∙ Uniprot:P98173 ∙ 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 FAM3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM3A 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				2	2	4
missense			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	3	2

Variants in FAM3A

This is a list of pathogenic ClinVar variants found in the FAM3A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154506852-C-T		not specified	Uncertain significance (Jan 04, 2024)
X-154506862-G-A			Benign (Oct 10, 2018)
X-154507467-T-C		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-154507483-G-A			Benign (Apr 11, 2018)
X-154507834-C-T			Likely benign (May 01, 2022)
X-154507842-G-A			Likely benign (Apr 01, 2022)
X-154508580-A-G		not specified	Uncertain significance (Sep 13, 2023)
X-154508586-T-C		not specified	Uncertain significance (Dec 09, 2023)
X-154511858-C-T			Likely benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM3A	protein_coding	protein_coding	ENST00000447601	9	11217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.669	0.327	97258	1	0	97259	0.00000514

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.927	79	106	0.746	0.00000961	1508
Missense in Polyphen		22	47.36	0.46453		666
Synonymous	-0.851	54	46.6	1.16	0.00000466	440
Loss of Function	2.27	1	7.88	0.127	4.99e-7	147

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)	0.0000159	0.0000122
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a defensin against invading fungal microorganisms.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.241
• hipred: N
• hipred_score: 0.423
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam3a

Gene ontology

• Biological process: antifungal humoral response;negative regulation of gluconeogenesis;regulation of lipid biosynthetic process;antimicrobial humoral immune response mediated by antimicrobial peptide;negative regulation of antifungal innate immune response
• Cellular component: cellular_component;extracellular region
• Molecular function: molecular_function