IGDCC4

immunoglobulin superfamily DCC subclass member 4, the group of Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 15:65381484-65422947

Links

ENSG00000103742 ∙ NCBI:57722 ∙ OMIM:616810 ∙ HGNC:13770 ∙ Uniprot:Q8TDY8 ∙ 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 IGDCC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGDCC4 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				3		3
missense			82	3		85
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	82	6	0

Variants in IGDCC4

This is a list of pathogenic ClinVar variants found in the IGDCC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65384019-G-T		not specified	Uncertain significance (Jul 12, 2022)
15-65384047-G-A			Likely benign (Jan 01, 2024)
15-65384185-C-T		not specified	Uncertain significance (Jan 17, 2024)
15-65384196-A-G		not specified	Uncertain significance (Dec 13, 2022)
15-65384203-A-C		not specified	Uncertain significance (Nov 08, 2022)
15-65384332-C-T		not specified	Uncertain significance (Dec 13, 2021)
15-65384370-G-A		not specified	Uncertain significance (Apr 08, 2024)
15-65384959-T-C		not specified	Uncertain significance (Feb 16, 2023)
15-65384991-G-A		not specified	Uncertain significance (Feb 12, 2024)
15-65385010-G-C		not specified	Uncertain significance (Jun 19, 2024)
15-65385010-G-T		not specified	Uncertain significance (Aug 15, 2023)
15-65385012-G-A		not specified	Uncertain significance (Dec 16, 2023)
15-65385121-C-G			Benign (Nov 15, 2017)
15-65385850-C-T		not specified	Uncertain significance (Jun 26, 2023)
15-65385922-G-A		not specified	Uncertain significance (Apr 14, 2022)
15-65385943-T-G		not specified	Uncertain significance (Sep 16, 2021)
15-65385952-G-A		not specified	Uncertain significance (May 03, 2023)
15-65385982-G-T		not specified	Uncertain significance (Mar 07, 2023)
15-65385986-G-T		not specified	Uncertain significance (Nov 21, 2023)
15-65386567-G-A		not specified	Uncertain significance (May 17, 2023)
15-65386621-C-T		not specified	Uncertain significance (Feb 27, 2023)
15-65386639-A-G		not specified	Uncertain significance (Sep 20, 2023)
15-65388514-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
15-65388541-C-T		not specified	Uncertain significance (Nov 10, 2022)
15-65388548-C-T		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGDCC4	protein_coding	protein_coding	ENST00000352385	20	41609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000236	1.00	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	588	719	0.818	0.0000431	7886
Missense in Polyphen		163	247.55	0.65846		2705
Synonymous	0.623	305	319	0.956	0.0000207	2706
Loss of Function	4.12	19	50.7	0.375	0.00000249	563

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000447	0.000447
Ashkenazi Jewish	0.00	0.00
East Asian	0.000508	0.000489
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.000508	0.000489
South Asian	0.000435	0.000425
Other	0.00101	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.666
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.52

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.736
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.170

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igdcc4

Gene ontology

• Cellular component: plasma membrane;integral component of membrane