IGSF21

immunoglobin superfamily member 21, the group of V-set domain containing

Basic information

Region (hg38): 1:18107797-18378483

Links

ENSG00000117154 ∙ NCBI:84966 ∙ ∙ HGNC:28246 ∙ Uniprot:Q96ID5 ∙ 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 IGSF21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF21 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					1	1
missense			29	3	2	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	3

Variants in IGSF21

This is a list of pathogenic ClinVar variants found in the IGSF21 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-18227930-C-T		not specified	Uncertain significance (Feb 12, 2024)
1-18227931-C-A		not specified	Uncertain significance (Oct 12, 2021)
1-18227948-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-18227985-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-18291882-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-18291950-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-18291951-G-T		not specified	Uncertain significance (Dec 28, 2022)
1-18334899-G-A		not specified	Uncertain significance (Sep 14, 2023)
1-18362168-C-T		not specified	Uncertain significance (Mar 28, 2024)
1-18362169-G-A		not specified	Uncertain significance (Nov 20, 2023)
1-18362190-C-A		not specified	Uncertain significance (Nov 17, 2023)
1-18365223-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-18365256-G-T		not specified	Uncertain significance (May 01, 2022)
1-18365266-T-C		not specified	Uncertain significance (Jul 21, 2022)
1-18365308-G-A		not specified	Uncertain significance (Sep 12, 2023)
1-18365320-G-A		not specified	Uncertain significance (Mar 07, 2023)
1-18365334-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-18365382-G-A		not specified	Likely benign (Nov 02, 2023)
1-18365392-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-18365404-C-A		not specified	Uncertain significance (Oct 05, 2023)
1-18365416-G-A			Benign (Apr 05, 2018)
1-18365425-G-A		not specified	Likely benign (Aug 02, 2022)
1-18365490-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-18365520-A-G		not specified	Uncertain significance (Jun 06, 2023)
1-18365526-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF21	protein_coding	protein_coding	ENST00000251296	10	270738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.209	0.791	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.324	296	312	0.948	0.0000215	2998
Missense in Polyphen		125	139.36	0.89697		1216
Synonymous	0.265	129	133	0.971	0.00000961	1004
Loss of Function	3.11	5	20.0	0.249	0.00000102	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in synaptic inhibition in the brain. Selectively regulates inhibitory presynaptic differentiation through interacting with presynaptic NRXN2. {ECO:0000250|UniProtKB:Q7TNR6}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.336
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.19

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.579
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igsf21
• 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)

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;synapse maturation
• Cellular component: cell-cell adherens junction;anchored component of external side of plasma membrane;presynaptic membrane;postsynaptic membrane;inhibitory synapse
• Molecular function: signaling receptor activity;protein homodimerization activity;cell adhesion molecule binding