IGDCC3

immunoglobulin superfamily DCC subclass member 3, the group of Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 15:65327127-65378002

Previous symbols: [ "PUNC" ]

Links

ENSG00000174498 ∙ NCBI:9543 ∙ OMIM:604184 ∙ HGNC:9700 ∙ Uniprot:Q8IVU1 ∙ 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 IGDCC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGDCC3 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	2	3
missense			65	3	1	69
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	65	4	3

Variants in IGDCC3

This is a list of pathogenic ClinVar variants found in the IGDCC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65328917-C-G		not specified	Uncertain significance (Jul 26, 2024)
15-65328934-G-A		not specified	Uncertain significance (Mar 25, 2024)
15-65328989-C-T		not specified	Uncertain significance (Feb 19, 2025)
15-65328995-C-T		not specified	Uncertain significance (Jun 17, 2024)
15-65329004-G-A		not specified	Uncertain significance (Oct 03, 2022)
15-65329013-C-G		not specified	Uncertain significance (May 15, 2023)
15-65329021-C-T		not specified	Uncertain significance (Sep 26, 2024)
15-65329036-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-65329063-G-A		not specified	Uncertain significance (Oct 29, 2021)
15-65329089-C-A		not specified	Uncertain significance (Sep 14, 2022)
15-65329115-T-A		not specified	Uncertain significance (Apr 07, 2023)
15-65329126-G-A		not specified	Likely benign (Sep 18, 2024)
15-65329418-G-C		not specified	Uncertain significance (Aug 14, 2024)
15-65329427-G-A		not specified	Uncertain significance (Dec 11, 2024)
15-65329434-A-C		not specified	Uncertain significance (Mar 28, 2023)
15-65329434-A-G		not specified	Uncertain significance (Jan 23, 2023)
15-65329463-C-T		not specified	Likely benign (Jan 03, 2022)
15-65329512-T-G		not specified	Uncertain significance (Mar 07, 2023)
15-65329529-G-A		not specified	Uncertain significance (Jun 12, 2023)
15-65329544-C-T		not specified	Uncertain significance (Jan 17, 2024)
15-65329550-C-T		not specified	Uncertain significance (Sep 24, 2024)
15-65329739-C-T		not specified	Uncertain significance (Jan 30, 2024)
15-65329763-A-G		not specified	Uncertain significance (Dec 04, 2024)
15-65329840-C-T		not specified	Uncertain significance (Aug 30, 2021)
15-65330295-G-A		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGDCC3	protein_coding	protein_coding	ENST00000327987	14	50914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-7	0.996	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.577	453	489	0.927	0.0000304	5127
Missense in Polyphen		118	163.46	0.72189		1823
Synonymous	0.299	212	218	0.974	0.0000144	1812
Loss of Function	2.58	16	31.7	0.505	0.00000168	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.0000947	0.0000924
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.0000555	0.0000544
South Asian	0.000526	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.698
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.86

Haploinsufficiency Scores

• pHI: 0.611
• hipred: Y
• hipred_score: 0.591
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.344

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igdcc3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: neuromuscular process controlling balance
• Cellular component: integral component of plasma membrane