IGFN1

protein-coding

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

Gene summary

Predicted to act upstream of or within myoblast differentiation and myoblast fusion. Predicted to be located in Z disc and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001164586.2

Inheritance

—

ClinVar variants

U:773B:125

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr1:201,190,824-201,228,952

External References & Databases

Ensembl (ENSG00000163395)

Transcript & Mutation Effects

hg38 • Region Span ~38.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IGFN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 826

not providedTotal: 63

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001164586.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	53 clinvar		55
missense			764 clinvar	71 clinvar		835
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar	1 clinvar		2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	773	125	0	898

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001164586.2	RefSeq	NP_001158058.1	23	MANE Select
ENST00000335211.9	Ensembl	ENSP00000334714.4	23	MANE Select
NM_001367841.1	RefSeq	NP_001354770.1	24	Standard
ENST00000295591.12	Ensembl	ENSP00000295591.9	24	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

protein binding

Cellular Component

nucleus
sarcomere
Z disc

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335211
Coding exons: 23
Length: 38128
Individuals with no LoFs: 125410
Homozygous LoFs: 1
Heterozygous LoFs: 337
Defined: 125748
p: 0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.225	1862	1.89e+3	0.985	0.0000997	23519
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0024	0.0024	notable
Latino/Admixed American	0.00070	0.00069	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0026	0.0026	notable
Finnish	0.00043	0.00042	rare
European (Non-Finnish)	0.0011	0.00099	notable
South Asian	0.0035	0.0032	notable
Other	0.0013	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.157
RVIS EVS: 6.49
RVIS percentile EVS: 99.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.113

Gene Damage Prediction

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