IGFN1

immunoglobulin like and fibronectin type III domain containing 1, the group of Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 1:201190824-201228952

Links

ENSG00000163395 ∙ NCBI:91156 ∙ OMIM:617309 ∙ HGNC:24607 ∙ Uniprot:Q86VF2 ∙ 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 IGFN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFN1 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				35		35
missense			399	37		436
nonsense			1			1
start loss						0
frameshift			1	1		2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	401	73	0

Variants in IGFN1

This is a list of pathogenic ClinVar variants found in the IGFN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201194154-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-201194177-C-A			Likely benign (Apr 01, 2025)
1-201194177-C-T		not specified	Uncertain significance (Nov 08, 2021)
1-201194178-C-G			Likely benign (Apr 01, 2025)
1-201194184-T-G		not specified	Uncertain significance (Oct 21, 2024)
1-201194188-C-A		not specified	Uncertain significance (Sep 27, 2021)
1-201194211-T-G		not specified	Uncertain significance (Jan 12, 2024)
1-201194220-G-C		not specified	Uncertain significance (Nov 10, 2024)
1-201194229-C-T		not specified	Uncertain significance (Oct 08, 2024)
1-201194249-C-G		not specified	Uncertain significance (Jul 16, 2024)
1-201194251-C-T			Likely benign (Jun 01, 2023)
1-201194252-G-A		not specified	Likely benign (Jan 23, 2024)
1-201194252-G-C		not specified	Uncertain significance (Mar 14, 2023)
1-201195847-G-T		not specified	Uncertain significance (Jan 06, 2023)
1-201195856-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-201195876-G-T		not specified	Uncertain significance (Feb 10, 2025)
1-201195893-G-A		not specified	Likely benign (Aug 02, 2021)
1-201195913-G-T		not specified	Uncertain significance (Nov 24, 2024)
1-201197221-A-T		not specified	Uncertain significance (Nov 13, 2024)
1-201197222-A-G		not specified	Uncertain significance (Jan 19, 2022)
1-201197224-A-C		not specified	Uncertain significance (Dec 05, 2024)
1-201197261-C-T		not specified	Uncertain significance (Nov 11, 2024)
1-201197275-T-C		not specified	Uncertain significance (Apr 22, 2024)
1-201197278-G-A		not specified	Uncertain significance (Feb 05, 2025)
1-201197284-G-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFN1	protein_coding	protein_coding	ENST00000335211	23	38128

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-51	0.000556	125410	1	337	125748	0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.225	1862	1.89e+3	0.985	0.0000997	23519
Missense in Polyphen		437	440.01	0.99315		5451
Synonymous	-1.17	785	744	1.05	0.0000429	7680
Loss of Function	2.10	92	116	0.790	0.00000554	1685

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00312	0.00310
Ashkenazi Jewish	0.00	0.00
East Asian	0.00257	0.00256
Finnish	0.000429	0.000416
European (Non-Finnish)	0.00109	0.000994
Middle Eastern	0.00257	0.00256
South Asian	0.00345	0.00324
Other	0.00132	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.157
• rvis_EVS: 6.49
• rvis_percentile_EVS: 99.88

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.146
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.113

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igfn1

Gene ontology

• Biological process: biological_process
• Cellular component: nucleus;sarcomere;Z disc
• Molecular function: protein binding