FNDC1

protein-coding

fibronectin type III domain containing 1, the group of Fibronectin type III domain containing

Gene summary

Predicted to act upstream of or within several processes, including cellular response to hypoxia; positive regulation of cardiac muscle cell apoptotic process; and positive regulation of protein phosphorylation. Predicted to be located in cell-cell junction; mitochondrial membrane; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FNDC2

MANE transcript

NM_032532.3

Inheritance

—

ClinVar variants

U:352B:34

Top phenotype

Scoliosis, isolated, susceptibility to, 1

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr6:159,169,400-159,272,108

External References & Databases

Ensembl (ENSG00000164694)

Transcript & Mutation Effects

hg38 • Region Span ~102.7 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 FNDC1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 354

not providedTotal: 19

Scoliosis, isolated, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032532.3. 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			4 clinvar	5 clinvar	6 clinvar	15
missense			345 clinvar	21 clinvar	2 clinvar	368
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	352	26	8	386

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032532.3	RefSeq	NP_115921.2	23	MANE Select
ENST00000297267.14	Ensembl	ENSP00000297267.9	23	MANE Select
ENST00000329629.8	Ensembl	ENSP00000333297.8	21	Standard
ENST00000906655.1	Ensembl	ENSP00000576714.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297267
Coding exons: 23
Length: 102713
Individuals with no LoFs: 124571
Homozygous LoFs: 0
Heterozygous LoFs: 76
Defined: 124647
p: 0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.234	1078	1.10e+3	0.980	0.0000683	11912
Missense (PolyPhen)		104	131.03	0.79371		1435
Synonymous	0.368	460	470	0.978	0.0000305	4087
Loss of Function	4.44	32	73.0	0.439	0.00000399	842

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00045	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00031	0.00030	rare
East Asian	0.00045	0.00028	rare
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.00033	0.00032	rare
South Asian	0.00047	0.00046	rare
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be an activator of G protein signaling. {ECO:0000250}.;

Recessive Scores

pRec: 0.0950

Intolerance Scores

LoFtool: 0.861
RVIS EVS: 2.67
RVIS percentile EVS: 98.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0843

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High