FAM3A

Chr X

FAM3 metabolism regulating signaling molecule A

Also known as: 2.19, DLD, DXS560S, XAP-7

NCBI Gene: 60343 ENSG00000071889 UniProt: P98173 OMIM: 300492

This gene encodes a cytokine-like protein that may function as a defensin against fungal pathogens and is involved in glucose and lipid metabolism regulation. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.602), but no established Mendelian diseases have been definitively associated with FAM3A mutations in current medical literature. Clinical significance of variants in this gene remains uncertain pending further research.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

LOEUF 0.60

Clinical Summary— FAM3A

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.67) — some intolerance to loss-of-function variants.

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ClinVar Variants

11 VUS of 59 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.60LOEUF

pLI 0.669

Z-score 2.27

OE 0.13 (0.04–0.60)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

0.93Z-score

OE missense 0.75 (0.62–0.90)

79 obs / 105.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.13 (0.04–0.60)

0≤0.351.4

Missense OE?0.75 (0.62–0.90)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 1 / 7.9Missense obs/exp: 79 / 105.8Syn Z: -0.85

ClinVar Variant Classifications

59 submitted variants in ClinVar

ClinVar

Classification Summary

VUS11

Likely Benign4

Benign2

Conflicting1

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	0	11	0	0	11
Likely Benign	0	2	0	2	4
Benign	0	0	0	2	2
Conflicting	—				1
Total	0	13	0	4	18

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

128 pathogenic / likely-pathogenic (of 144) ClinVar copy-number / structural variants overlap FAM3A — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →