FNDC3B

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

Basic information

Region (hg38): 3:172039577-172401669

Links

ENSG00000075420 ∙ NCBI:64778 ∙ OMIM:611909 ∙ HGNC:24670 ∙ Uniprot:Q53EP0 ∙ 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 FNDC3B gene.

• Inborn genetic diseases (29 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNDC3B 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				1	1	2
missense			29		1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	1	3

Variants in FNDC3B

This is a list of pathogenic ClinVar variants found in the FNDC3B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-172247615-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-172247692-T-C		not specified	Uncertain significance (Oct 12, 2022)
3-172247711-C-A		not specified	Uncertain significance (Dec 20, 2023)
3-172247762-T-C		not specified	Uncertain significance (Jun 10, 2022)
3-172251287-C-G		FNDC3B-related disorder	Benign (Oct 29, 2019)
3-172251425-A-G		not specified	Uncertain significance (Feb 15, 2023)
3-172251427-G-C		not specified	Uncertain significance (Jan 03, 2024)
3-172251436-C-T		not specified	Uncertain significance (Aug 21, 2023)
3-172251438-T-C		FNDC3B-related disorder	Benign (Dec 11, 2019)
3-172251439-A-G		not specified	Uncertain significance (Dec 14, 2021)
3-172251521-C-T		not specified	Uncertain significance (Jul 20, 2022)
3-172251522-G-C		FNDC3B-related disorder	Benign (Dec 16, 2019)
3-172295469-C-T		not specified	Uncertain significance (May 27, 2022)
3-172307385-G-A		not specified	Uncertain significance (May 27, 2022)
3-172307438-C-T		FNDC3B-related disorder	Benign (Jan 01, 2024)
3-172329026-G-A		not specified	Likely benign (Dec 20, 2023)
3-172329051-G-T		FNDC3B-related disorder	Benign (Nov 08, 2019)
3-172329066-A-G		not specified	Uncertain significance (Jan 22, 2024)
3-172329071-T-C		FNDC3B-related disorder	Benign (Oct 30, 2019)
3-172330709-T-A		not specified	Uncertain significance (Dec 14, 2023)
3-172330714-A-G		not specified	Uncertain significance (Mar 13, 2023)
3-172335000-G-A		FNDC3B-related disorder	Likely benign (Dec 01, 2022)
3-172335071-G-C		not specified	Uncertain significance (Jun 18, 2021)
3-172337332-C-G		not specified	Uncertain significance (Jan 12, 2024)
3-172337341-G-T		not specified	Uncertain significance (Aug 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNDC3B	protein_coding	protein_coding	ENST00000336824	25	362038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.18e-12	125745	0	2	125747	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	551	690	0.799	0.0000378	7833
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a positive regulator of adipogenesis. {ECO:0000269|PubMed:15564382}.
• 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: 0.105

Intolerance Scores

• loftool: 0.149
• rvis_EVS: -0.63
• rvis_percentile_EVS: 16.77

Haploinsufficiency Scores

• pHI: 0.414
• hipred: Y
• hipred_score: 0.591
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fndc3b
• Phenotype: skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: RNA binding