FNDC3B

protein-coding

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

Gene summary

Enables RNA binding activity. Predicted to act upstream of or within several processes, including negative regulation of osteoblast differentiation; substrate adhesion-dependent cell spreading; and type II pneumocyte differentiation. Predicted to be located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_022763.4

Inheritance

—

ClinVar variants

U:149B:11

Top phenotype

FNDC3B-related disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr3:172,039,578-172,401,669

External References & Databases

Ensembl (ENSG00000075420)

Transcript & Mutation Effects

hg38 • Region Span ~362.1 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 FNDC3B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 130

FNDC3B-related disorderTotal: 11

not providedTotal: 7

Familial meningiomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022763.4. 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			3 clinvar	4 clinvar	3 clinvar	10
missense			133 clinvar	1 clinvar	3 clinvar	137
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	149	5	6	160

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 117 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022763.4	RefSeq	NP_073600.3	25	MANE Select
ENST00000415807.7	Ensembl	ENSP00000411242.2	25	MANE Select
NM_001135095.2	RefSeq	NP_001128567.1	25	Standard
ENST00000336824.8	Ensembl	ENSP00000338523.4	25	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

Molecular Function

RNA binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000336824
Coding exons: 25
Length: 362038
Individuals with no LoFs: 125745
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125747
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.87	551	690	0.799	0.0000378	7833
Missense (PolyPhen)		75	160.48	0.46735		1794
Synonymous	-0.389	274	266	1.03	0.0000167	2360
Loss of Function	7.74	0	69.8	0.00	0.00000379	805

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a positive regulator of adipogenesis. {ECO:0000269|PubMed:15564382}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.149
RVIS EVS: -0.63
RVIS percentile EVS: 16.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.160

Gene Damage Prediction

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