FNDC9

protein-coding

fibronectin type III domain containing 9, the group of Fibronectin type III domain containing

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C5orf40

MANE transcript

NM_001001343.4

Inheritance

—

ClinVar variants

U:32B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr5:157,341,598-157,345,677

External References & Databases

Ensembl (ENSG00000172568)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 FNDC9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001343.4. 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		3
missense			32 clinvar	5 clinvar		37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	8	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001343.4	RefSeq	NP_001001343.2	1	MANE Select
ENST00000312349.5	Ensembl	ENSP00000310594.4	1	MANE Select
ENST00000520782.1	Ensembl	ENSP00000429434.1	1	Standard
ENST00001135129.1	Ensembl	ENSP00000806140.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000312349
Coding exons: 1
Length: 4122
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0286	132	133	0.993	0.00000714	1463
Missense (PolyPhen)		35	43.038	0.81323		515
Synonymous	-0.540	63	57.8	1.09	0.00000359	451
Loss of Function	0.967	4	6.70	0.597	4.37e-7	60

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.33
RVIS percentile EVS: 73.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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