FAM3A

protein-coding

FAM3 metabolism regulating signaling molecule A

Gene summary

This gene encodes a cytokine-like protein. The expression of this gene may be regulated by peroxisome proliferator-activated receptor gamma, and the encoded protein may be involved in the regulation of glucose and lipid metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

MANE transcript

NM_021806.4

Inheritance

—

ClinVar variants

U:39B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chrX:154,506,159-154,516,242

External References & Databases

Ensembl (ENSG00000071889)

Transcript & Mutation Effects

hg38 • Region Span ~10.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM3A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 13

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021806.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	2 clinvar	2 clinvar	11
missense			17 clinvar	3 clinvar		20
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			14 clinvar			14
Total	0	0	39	5	2	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 85 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021806.4	RefSeq	NP_068578.2	9	MANE Select
ENST00000447601.7	Ensembl	ENSP00000416146.2	9	MANE Select
NM_001171132.3	RefSeq	NP_001164603.1	9	Standard
NM_001171133.3	RefSeq	NP_001164604.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

molecular_function

Cellular Component

cellular_component
extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000447601
Coding exons: 9
Length: 11217
Individuals with no LoFs: 97258
Homozygous LoFs: 1
Heterozygous LoFs: 0
Defined: 97259
p: 0.00000514

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.927	79	106	0.746	0.00000961	1508
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000016	0.000012	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.132

Gene Damage Prediction

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