IGSF9

protein-coding

immunoglobulin superfamily member 9, the group of Fibronectin type III domain containing|I-set domain containing

Gene summary

Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in axon guidance; dendrite self-avoidance; and homophilic cell-cell adhesion. Predicted to act upstream of or within dendrite development and regulation of synapse organization. Predicted to be located in dendrite and inhibitory synapse. Predicted to be active in axon and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001135050.2

Inheritance

—

ClinVar variants

U:222B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr1:159,927,039-159,945,613

External References & Databases

Ensembl (ENSG00000085552)

Transcript & Mutation Effects

hg38 • Region Span ~18.6 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 IGSF9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 207

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001135050.2. 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			5 clinvar	4 clinvar		9
missense			210 clinvar	7 clinvar		217
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	222	11	0	233

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001135050.2	RefSeq	NP_001128522.1	20	MANE Select
ENST00000368094.6	Ensembl	ENSP00000357073.1	20	MANE Select
NM_020789.4	RefSeq	NP_065840.2	20	Standard
ENST00000361509.7	Ensembl	ENSP00000355049.3	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

homophilic cell adhesion via plasma membrane adhesion molecules
axon guidance
dendrite development
regulation of synapse organization
dendrite self-avoidance

Molecular Function

cell-cell adhesion mediator activity

Cellular Component

plasma membrane
integral component of membrane
cell junction
axon
dendrite

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368094
Coding exons: 20
Length: 18558
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 125746
p: 0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.754	629	685	0.919	0.0000428	7303
Missense (PolyPhen)		205	233.62	0.8775		2543
Synonymous	0.788	267	284	0.941	0.0000170	2625
Loss of Function	3.32	28	54.4	0.514	0.00000325	531

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00079	0.00074	rare
Latino/Admixed American	0.00013	0.00012	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00040	0.00039	rare
South Asian	0.00045	0.00042	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions in dendrite outgrowth and synapse maturation. {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.748
RVIS EVS: 0.14
RVIS percentile EVS: 63.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.823

Gene Damage Prediction

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