FNDC4

fibronectin type III domain containing 4, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 2:27491883-27495200

Links

ENSG00000115226 ∙ NCBI:64838 ∙ OMIM:611905 ∙ HGNC:20239 ∙ Uniprot:Q9H6D8 ∙ 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 FNDC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FNDC4 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in FNDC4

This is a list of pathogenic ClinVar variants found in the FNDC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27493445-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-27494028-C-T		not specified	Uncertain significance (Apr 01, 2024)
2-27494056-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-27494591-G-A		not specified	Uncertain significance (Jun 17, 2024)
2-27494639-C-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FNDC4	protein_coding	protein_coding	ENST00000264703	6	3363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.881	0.119	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	94	145	0.647	0.00000892	1488
Missense in Polyphen		32	49.976	0.6403		515
Synonymous	-0.466	60	55.6	1.08	0.00000314	504
Loss of Function	2.84	1	11.3	0.0883	6.12e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an anti-inflammatory factor in the intestine and colon. Binds to and acts on macrophages to downregulate pro- inflammatory gene expression. Affects key macrophage functions, including phagocytosis, by downregulating many key pathways for macrophage activation, partly via by STAT3 activation and signaling. May be required to dampen the immunological response in colitis. {ECO:0000250|UniProtKB:Q3TR08}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.271
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.323
• hipred: Y
• hipred_score: 0.800
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fndc4
• Phenotype: digestive/alimentary phenotype; immune system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of inflammatory response;response to transforming growth factor beta
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum;plasma membrane;integral component of membrane