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.

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.

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				2	1	3
missense			74	6		80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	8	1

Variants in IGSF9

This is a list of pathogenic ClinVar variants found in the IGSF9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-159927364-T-C		not specified	Uncertain significance (Aug 11, 2024)
1-159927418-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-159927466-G-A		not specified	Uncertain significance (Aug 27, 2024)
1-159927490-G-A		not specified	Uncertain significance (May 24, 2023)
1-159927790-G-A		not specified	Uncertain significance (Dec 06, 2021)
1-159927808-G-C		not specified	Uncertain significance (Aug 14, 2023)
1-159928180-G-A		not specified	Uncertain significance (Dec 20, 2022)
1-159928444-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-159928461-G-T		not specified	Uncertain significance (Dec 27, 2022)
1-159928479-G-A		not specified	Likely benign (Jan 16, 2024)
1-159928510-G-A		not specified	Uncertain significance (May 28, 2023)
1-159928512-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-159928558-G-A		not specified	Uncertain significance (Jul 09, 2024)
1-159928582-T-C		not specified	Uncertain significance (Jun 10, 2024)
1-159928614-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-159928626-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-159928660-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-159928683-T-A		not specified	Uncertain significance (May 05, 2022)
1-159928704-G-T		not specified	Uncertain significance (Mar 20, 2023)
1-159928705-G-T		not specified	Uncertain significance (Feb 28, 2024)
1-159928710-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-159928747-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-159928753-G-C		not specified	Uncertain significance (Oct 12, 2024)
1-159928753-G-T		not specified	Uncertain significance (Mar 18, 2024)
1-159928794-C-T		not specified	Likely benign (Aug 02, 2022)

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