IGSF11

immunoglobulin superfamily member 11, the group of IgCAM CXADR-related subfamily|I-set domain containing

Basic information

Region (hg38): 3:118900557-119146068

Links

ENSG00000144847 ∙ NCBI:152404 ∙ OMIM:608351 ∙ HGNC:16669 ∙ Uniprot:Q5DX21 ∙ 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 IGSF11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF11 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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in IGSF11

This is a list of pathogenic ClinVar variants found in the IGSF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-118902563-G-C		not specified	Uncertain significance (Dec 05, 2022)
3-118902569-G-A		not specified	Uncertain significance (Aug 30, 2022)
3-118902576-T-A		not specified	Uncertain significance (Feb 28, 2024)
3-118902588-T-G		not specified	Uncertain significance (Nov 18, 2024)
3-118902629-G-A		not specified	Uncertain significance (Jan 05, 2022)
3-118902647-C-G		not specified	Uncertain significance (Aug 27, 2024)
3-118902681-C-T		not specified	Uncertain significance (Jun 10, 2024)
3-118902710-T-C		not specified	Uncertain significance (Oct 08, 2024)
3-118902722-A-G		not specified	Uncertain significance (Dec 05, 2022)
3-118902758-T-A		not specified	Uncertain significance (Mar 16, 2022)
3-118902761-G-A		not specified	Uncertain significance (Jul 17, 2024)
3-118902776-A-T		not specified	Uncertain significance (Aug 16, 2022)
3-118902842-T-C		not specified	Uncertain significance (Feb 06, 2024)
3-118902857-C-T		not specified	Uncertain significance (May 30, 2023)
3-118902872-T-C		not specified	Uncertain significance (May 14, 2024)
3-118902905-G-T		not specified	Uncertain significance (Sep 10, 2024)
3-118902939-A-C		not specified	Uncertain significance (Jun 07, 2023)
3-118902959-T-C		not specified	Uncertain significance (Jun 23, 2023)
3-118904700-A-G		not specified	Uncertain significance (Jul 13, 2021)
3-118904721-T-G		not specified	Uncertain significance (Apr 16, 2024)
3-118904753-C-T		not specified	Uncertain significance (Apr 22, 2022)
3-118905692-G-A		not specified	Uncertain significance (Jan 26, 2022)
3-118926191-G-A		not specified	Uncertain significance (Apr 29, 2024)
3-118928544-C-T		not specified	Uncertain significance (May 02, 2024)
3-118928605-T-G		not specified	Uncertain significance (Dec 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF11	protein_coding	protein_coding	ENST00000393775	7	245512

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00100	0.988	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	184	236	0.779	0.0000119	2774
Missense in Polyphen		47	83.416	0.56344		972
Synonymous	-1.26	107	91.6	1.17	0.00000475	916
Loss of Function	2.24	8	18.4	0.435	0.00000105	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000243	0.000237
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a cell adhesion molecule through homophilic interaction. Stimulates cell growth. {ECO:0000269|PubMed:15795899, ECO:0000269|PubMed:16108831}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.719
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.287
• hipred: Y
• hipred_score: 0.653
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf11
• 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); reproductive system phenotype

Gene ontology

• Biological process: cell adhesion;regulation of growth
• Cellular component: plasma membrane;integral component of membrane