FNDC3A

protein-coding

fibronectin type III domain containing 3A, the group of Fibronectin type III domain containing

Gene summary

Enables RNA binding activity. Predicted to be involved in spermatid development. Predicted to act upstream of or within Sertoli cell development; cell-cell adhesion; and fertilization. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FNDC3

MANE transcript

NM_001079673.2

Inheritance

—

ClinVar variants

U:149B:11

Top phenotype

FNDC3A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr13:48,975,912-49,209,779

External References & Databases

Ensembl (ENSG00000102531)

Transcript & Mutation Effects

hg38 • Region Span ~233.9 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 FNDC3A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 135

not providedTotal: 8

FNDC3A-related disorderTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079673.2. 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			2 clinvar	4 clinvar	2 clinvar	8
missense			138 clinvar	4 clinvar	1 clinvar	143
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	149	8	3	160

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079673.2	RefSeq	NP_001073141.1	25	MANE Select
ENST00000492622.6	Ensembl	ENSP00000417257.1	25	MANE Select
NM_001278438.2	RefSeq	NP_001265367.1	25	Standard
NM_014923.5	RefSeq	NP_055738.3	24	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
miR-targeted genes in squamous cell - TarBase

Biological Process

spermatid development
fertilization
Sertoli cell development
cell-cell adhesion

Molecular Function

RNA binding

Cellular Component

Golgi membrane
acrosomal vesicle
Golgi apparatus
cytosol
vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000492622
Coding exons: 25
Length: 233868
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125738
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	527	635	0.829	0.0000320	7796
Missense (PolyPhen)		54	114.64	0.47104		1328
Synonymous	0.473	199	208	0.958	0.00000997	2304
Loss of Function	6.58	8	65.4	0.122	0.00000337	813

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates spermatid-Sertoli adhesion during spermatogenesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.493

Intolerance Scores

LoFtool: 0.375
RVIS EVS: -1.55
RVIS percentile EVS: 3.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.470

Gene Damage Prediction

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