FAM3D

protein-coding

FAM3 metabolism regulating signaling molecule D

Gene summary

Predicted to enable cytokine activity. Involved in negative regulation of insulin secretion. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_138805.3

Inheritance

—

ClinVar variants

U:35B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr3:58,633,946-58,666,834

External References & Databases

Ensembl (ENSG00000198643)

Transcript & Mutation Effects

hg38 • Region Span ~32.9 kb

Loading mutation effect viewer...

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 FAM3D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138805.3. 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			1 clinvar	1 clinvar		2
missense			34 clinvar	3 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	4	0	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138805.3	RefSeq	NP_620160.1	9	MANE Select
ENST00000358781.7	Ensembl	ENSP00000351632.2	9	MANE Select
ENST00000482623.5	Ensembl	ENSP00000418414.1	3	Standard
ENST00000483787.5	Ensembl	ENSP00000417099.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of signaling receptor activity
negative regulation of insulin secretion
negative regulation of glucagon secretion

Molecular Function

cytokine activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358781
Coding exons: 9
Length: 32903
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125748
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.205	131	138	0.951	0.00000793	1476
Missense (PolyPhen)		51	57.855	0.88151		624
Synonymous	-1.25	62	50.7	1.22	0.00000325	406
Loss of Function	1.63	8	14.7	0.542	8.73e-7	149

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0952

Intolerance Scores

LoFtool: 0.642
RVIS EVS: 0.26
RVIS percentile EVS: 70.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.450

Gene Damage Prediction

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