IGSF9B

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

Basic information

Region (hg38): 11:133896438-133956968

Previous symbols: [ "MIR4697HG" ]

Links

ENSG00000080854 ∙ NCBI:22997 ∙ OMIM:613773 ∙ HGNC:32326 ∙ Uniprot:Q9UPX0 ∙ 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 IGSF9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF9B 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				4	1	5
missense				1	1	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	0	5	2

Variants in IGSF9B

This is a list of pathogenic ClinVar variants found in the IGSF9B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-133919890-C-T			Benign (May 08, 2018)
11-133920180-C-T			Likely benign (May 08, 2018)
11-133920183-G-A		IGSF9B-related condition	Uncertain significance (May 08, 2024)
11-133920248-G-A			Likely benign (Jul 13, 2018)
11-133920493-G-T			Likely benign (Mar 01, 2023)
11-133921088-G-A			Benign (Jul 13, 2018)
11-133921271-C-T			Likely benign (Oct 01, 2022)
11-133931561-G-T			Benign/Likely benign (Feb 01, 2023)
11-133935762-G-A		not specified	Likely benign (Nov 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF9B	protein_coding	protein_coding	ENST00000533871	20	48422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.866	0.134	124630	0	21	124651	0.0000842

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	690	909	0.759	0.0000608	9111
Missense in Polyphen		235	361.47	0.65013		3614
Synonymous	-0.171	405	401	1.01	0.0000293	3064
Loss of Function	5.90	13	63.9	0.204	0.00000365	660

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000357	0.000345
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.0000526	0.0000464
European (Non-Finnish)	0.0000839	0.0000796
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000753	0.0000654
Other	0.000185	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transmembrane protein which is abundantly expressed in interneurons, where it may regulate inhibitory synapse development. May mediate homophilic cell adhesion. {ECO:0000250|UniProtKB:D3ZB51, ECO:0000250|UniProtKB:E9PZ19}.
• Pathway: Vitamin D Receptor Pathway (Consensus)

Haploinsufficiency Scores

• pHI: 0.133
• hipred: Y
• hipred_score: 0.755
• ghis: 0.556

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf9b

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;nervous system development;positive regulation of inhibitory postsynaptic potential;synaptic membrane adhesion
• Cellular component: postsynaptic density;integral component of membrane;cell junction;dendrite;neuronal cell body;postsynaptic membrane;inhibitory synapse;GABA-ergic synapse;postsynaptic specialization of symmetric synapse
• Molecular function: kinase binding