IGSF9

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

Basic information

Region (hg38): 1:159927039-159945613

Links

ENSG00000085552 ∙ NCBI:57549 ∙ OMIM:609738 ∙ HGNC:18132 ∙ Uniprot:Q9P2J2 ∙ 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 IGSF9 gene.

• not_specified (184 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135050.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			176	7		183
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	176	11	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF9	protein_coding	protein_coding	ENST00000368094	20	18558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.44e-12	1.00	125665	0	81	125746	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.754	629	685	0.919	0.0000428	7303
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000912	0.000865
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000223	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000404	0.000387
Middle Eastern	0.000223	0.000217
South Asian	0.000451	0.000425
Other	0.000193	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.256
• hipred: N
• hipred_score: 0.432
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.823

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf9
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;axon guidance;dendrite development;regulation of synapse organization;dendrite self-avoidance
• Cellular component: plasma membrane;integral component of membrane;cell junction;axon;dendrite;inhibitory synapse
• Molecular function: cell-cell adhesion mediator activity