FNDC9

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

Basic information

Region (hg38): 5:157341598-157345677

Previous symbols: [ "C5orf40" ]

Links

ENSG00000172568 ∙ NCBI:408263 ∙ ∙ HGNC:33547 ∙ Uniprot:Q8TBE3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FNDC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNDC9 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			17	2	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	5	1

Variants in FNDC9

This is a list of pathogenic ClinVar variants found in the FNDC9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-157342888-C-T		not specified	Uncertain significance (Mar 08, 2025)
5-157342897-C-T		not specified	Uncertain significance (Dec 25, 2024)
5-157342905-C-A		not specified	Uncertain significance (Jun 21, 2023)
5-157342907-C-A		not specified	Uncertain significance (Nov 17, 2022)
5-157342907-C-G		not specified	Likely benign (Feb 16, 2025)
5-157342908-C-T		not specified	Uncertain significance (Sep 30, 2024)
5-157342918-C-T		not specified	Uncertain significance (Jan 23, 2025)
5-157342923-G-C		not specified	Uncertain significance (Feb 12, 2025)
5-157342944-G-C		not specified	Uncertain significance (Oct 24, 2024)
5-157342956-A-G		not specified	Likely benign (Dec 19, 2022)
5-157342961-A-C			Likely benign (Dec 01, 2021)
5-157342984-G-A		not specified	Uncertain significance (May 21, 2024)
5-157342998-A-T		not specified	Uncertain significance (Dec 20, 2021)
5-157343040-G-A		not specified	Uncertain significance (Aug 15, 2024)
5-157343100-G-A		not specified	Uncertain significance (Aug 26, 2024)
5-157343109-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-157343145-A-G			Likely benign (Dec 01, 2024)
5-157343212-G-A		not specified	Uncertain significance (Nov 25, 2024)
5-157343249-A-T		not specified	Uncertain significance (May 03, 2023)
5-157343250-T-C		not specified	Uncertain significance (Jan 31, 2022)
5-157343277-T-C		not specified	Uncertain significance (Jan 24, 2023)
5-157343346-T-C		not specified	Uncertain significance (Jan 08, 2025)
5-157343358-G-A		not specified	Uncertain significance (Mar 20, 2024)
5-157343359-A-T		not specified	Uncertain significance (Mar 20, 2024)
5-157343367-G-A			Likely benign (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNDC9	protein_coding	protein_coding	ENST00000312349	1	4122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00738	0.787	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0286	132	133	0.993	0.00000714	1463
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000879	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.248
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fndc9

Gene ontology

• Cellular component: integral component of membrane