FNDC3A

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

Basic information

Region (hg38): 13:48975912-49209779

Previous symbols: [ "FNDC3" ]

Links

ENSG00000102531 ∙ NCBI:22862 ∙ OMIM:615794 ∙ HGNC:20296 ∙ Uniprot:Q9Y2H6 ∙ 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 FNDC3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNDC3A 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					2	2
missense			66	4	1	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	66	4	3

Variants in FNDC3A

This is a list of pathogenic ClinVar variants found in the FNDC3A region.

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

Position	Type	Phenotype	Significance	ClinVar
13-49006236-A-G		not specified	Uncertain significance (Aug 12, 2021)
13-49006243-T-C		not specified	Uncertain significance (Aug 20, 2024)
13-49006249-T-G		not specified	Uncertain significance (May 05, 2023)
13-49075281-T-C			Likely benign (Nov 01, 2022)
13-49075304-G-A		not specified	Uncertain significance (Aug 08, 2023)
13-49075354-G-C		not specified	Uncertain significance (Nov 18, 2022)
13-49114723-G-A		not specified	Uncertain significance (Dec 21, 2023)
13-49131203-A-G			Benign (Dec 31, 2019)
13-49131239-C-G		not specified	Uncertain significance (Nov 12, 2021)
13-49131288-A-C		not specified	Uncertain significance (Feb 07, 2023)
13-49131302-G-A		not specified	Uncertain significance (Mar 07, 2025)
13-49131365-G-A		not specified	Uncertain significance (Jul 05, 2023)
13-49136337-C-T		not specified	Uncertain significance (Nov 07, 2023)
13-49136340-T-G		not specified	Uncertain significance (Jan 22, 2024)
13-49136377-C-G		not specified	Uncertain significance (Jul 11, 2023)
13-49136379-A-T		not specified	Uncertain significance (Sep 06, 2022)
13-49136419-G-T		not specified	Uncertain significance (May 13, 2024)
13-49136425-G-A		not specified	Uncertain significance (May 31, 2022)
13-49136520-G-C		not specified	Uncertain significance (Mar 27, 2023)
13-49136583-G-A		not specified	Likely benign (Jul 12, 2022)
13-49138744-A-T		FNDC3A-related disorder	Likely benign (Jan 05, 2023)
13-49138752-G-C		not specified	Uncertain significance (Jun 11, 2021)
13-49138755-G-A		not specified	Uncertain significance (Dec 27, 2023)
13-49145779-C-T		not specified	Uncertain significance (Jul 02, 2024)
13-49145783-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNDC3A	protein_coding	protein_coding	ENST00000492622	25	233868

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000228	125728	0	10	125738	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	527	635	0.829	0.0000320	7796
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000374	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates spermatid-Sertoli adhesion during spermatogenesis. {ECO:0000250}.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.493

Intolerance Scores

• loftool: 0.375
• rvis_EVS: -1.55
• rvis_percentile_EVS: 3.28

Haploinsufficiency Scores

• pHI: 0.449
• hipred: N
• hipred_score: 0.426
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.470

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fndc3a
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: spermatid development;fertilization;Sertoli cell development;cell-cell adhesion
• Cellular component: Golgi membrane;acrosomal vesicle;Golgi apparatus;cytosol;vesicle membrane;membrane;integral component of membrane
• Molecular function: RNA binding