FNDC1

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

Basic information

Region (hg38): 6:159169400-159272108

Previous symbols: [ "FNDC2" ]

Links

ENSG00000164694 ∙ NCBI:84624 ∙ OMIM:609991 ∙ HGNC:21184 ∙ Uniprot:Q4ZHG4 ∙ 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 FNDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNDC1 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				5	5	10
missense			148	15	2	165
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	148	20	7

Variants in FNDC1

This is a list of pathogenic ClinVar variants found in the FNDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-159169628-C-G		not specified	Uncertain significance (Mar 07, 2024)
6-159169681-G-T		not specified	Uncertain significance (Oct 20, 2021)
6-159169697-C-A		not specified	Uncertain significance (Jul 28, 2021)
6-159169702-T-A		not specified	Uncertain significance (Jul 28, 2021)
6-159197433-G-C		not specified	Uncertain significance (Jul 06, 2021)
6-159197499-G-A		not specified	Uncertain significance (Nov 15, 2021)
6-159197515-C-A		not specified	Uncertain significance (Sep 21, 2023)
6-159197593-C-T		not specified	Uncertain significance (Oct 13, 2023)
6-159197622-G-T		not specified	Uncertain significance (Sep 14, 2022)
6-159200004-G-T		not specified	Uncertain significance (Jun 02, 2023)
6-159200032-A-G		not specified	Uncertain significance (Jun 28, 2022)
6-159200052-C-T		not specified	Uncertain significance (Mar 01, 2024)
6-159200076-C-T		not specified	Uncertain significance (Oct 05, 2023)
6-159200525-T-C		not specified	Uncertain significance (Sep 07, 2022)
6-159200575-G-A		not specified	Uncertain significance (Jul 26, 2021)
6-159214977-C-T		not specified	Uncertain significance (Jul 25, 2023)
6-159214978-G-A		not specified	Uncertain significance (Sep 01, 2021)
6-159214983-C-T		not specified	Uncertain significance (Apr 27, 2022)
6-159214984-G-A		not specified	Uncertain significance (Aug 16, 2022)
6-159215055-T-C		not specified	Uncertain significance (Feb 28, 2024)
6-159215059-G-A		not specified	Uncertain significance (Apr 06, 2022)
6-159215085-A-T		not specified	Uncertain significance (Mar 27, 2023)
6-159215091-C-T		not specified	Uncertain significance (Nov 09, 2022)
6-159215095-A-G		not specified	Uncertain significance (Jun 06, 2023)
6-159215135-C-T			Benign (Jan 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNDC1	protein_coding	protein_coding	ENST00000297267	23	102713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.78e-12	1.00	124571	0	76	124647	0.000305

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.234	1078	1.10e+3	0.980	0.0000683	11912
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000645	0.000632
Ashkenazi Jewish	0.000307	0.000298
East Asian	0.000445	0.000278
Finnish	0.000187	0.000186
European (Non-Finnish)	0.000329	0.000319
Middle Eastern	0.000445	0.000278
South Asian	0.000469	0.000458
Other	0.000181	0.000165

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.270
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fndc1

Gene ontology

• Cellular component: extracellular region;nuclear speck