IGSF22

immunoglobulin superfamily member 22, the group of Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 11:18704311-18726230

Links

ENSG00000179057 ∙ NCBI:283284 ∙ ∙ HGNC:26750 ∙ Uniprot:Q8N9C0 ∙ 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 IGSF22 gene.

• Inborn genetic diseases (57 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGSF22 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			58	1	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	58	2	2

Variants in IGSF22

This is a list of pathogenic ClinVar variants found in the IGSF22 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18704503-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-18704529-T-C		not specified	Uncertain significance (Aug 23, 2021)
11-18705953-C-G		not specified	Uncertain significance (Sep 06, 2022)
11-18705985-T-C		not specified	Uncertain significance (Dec 03, 2021)
11-18705991-G-A		not specified	Uncertain significance (Dec 13, 2023)
11-18706082-G-C		not specified	Uncertain significance (Nov 09, 2023)
11-18706090-G-T		not specified	Uncertain significance (Nov 09, 2023)
11-18706968-C-T		not specified	Uncertain significance (Jan 27, 2022)
11-18707000-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-18707012-G-C			Uncertain significance (Jul 18, 2021)
11-18707043-TGAA-T			Likely benign (Sep 01, 2022)
11-18707081-C-T		not specified	Uncertain significance (Feb 27, 2024)
11-18707090-C-T		not specified	Uncertain significance (Sep 21, 2023)
11-18707190-G-T		not specified	Uncertain significance (Dec 08, 2023)
11-18707198-G-C		not specified	Uncertain significance (Apr 25, 2022)
11-18707809-A-G		not specified	Uncertain significance (Jun 22, 2021)
11-18707854-A-C		not specified	Uncertain significance (Jan 31, 2023)
11-18707885-G-A		not specified	Uncertain significance (Jan 24, 2023)
11-18707929-G-T		not specified	Uncertain significance (Dec 28, 2023)
11-18707941-C-T			Benign (Jul 01, 2022)
11-18707946-C-G		not specified	Uncertain significance (Feb 28, 2023)
11-18708244-C-T		not specified	Uncertain significance (Sep 14, 2022)
11-18708253-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-18708289-G-T		not specified	Uncertain significance (Dec 21, 2022)
11-18709405-G-A		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGSF22	protein_coding	protein_coding	ENST00000513874	22	21926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.96e-41	3.74e-7	124415	1	691	125107	0.00277

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	688	782	0.880	0.0000457	8711
Missense in Polyphen		136	189.3	0.71842		2406
Synonymous	3.33	243	319	0.763	0.0000199	2617
Loss of Function	-0.375	60	56.9	1.05	0.00000306	667

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00408	0.00401
Ashkenazi Jewish	0.00	0.00
East Asian	0.00184	0.00184
Finnish	0.000371	0.000371
European (Non-Finnish)	0.00464	0.00462
Middle Eastern	0.00184	0.00184
South Asian	0.000985	0.000981
Other	0.00248	0.00246

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 3.99
• rvis_percentile_EVS: 99.66

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.170
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.454

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: muscle contraction;skeletal muscle thin filament assembly;skeletal muscle myosin thick filament assembly;sarcomere organization;cardiac muscle fiber development;cardiac myofibril assembly;cardiac muscle tissue morphogenesis;striated muscle myosin thick filament assembly
• Cellular component: striated muscle thin filament;sarcomere;Z disc;M band
• Molecular function: structural constituent of muscle;actin filament binding;muscle alpha-actinin binding