IGDCC3

protein-coding

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

Gene summary

Predicted to be involved in cell-cell adhesion. Predicted to act upstream of or within neuromuscular process controlling balance. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PUNC

MANE transcript

NM_004884.4

Inheritance

—

ClinVar variants

U:126B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr15:65,327,127-65,378,002

External References & Databases

Ensembl (ENSG00000174498)

Transcript & Mutation Effects

hg38 • Region Span ~50.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IGDCC3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 126

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004884.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	2 clinvar	4
missense			124 clinvar	3 clinvar	1 clinvar	128
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	126	4	3	133

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004884.4	RefSeq	NP_004875.2	14	MANE Select
ENST00000327987.9	Ensembl	ENSP00000332773.4	14	MANE Select
ENST00000558354.5	Ensembl	ENSP00000454105.1	11	Standard
ENST00000559058.1	Ensembl	ENSP00000452838.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

neuromuscular process controlling balance

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327987
Coding exons: 14
Length: 50914
Individuals with no LoFs: 125707
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125748
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.577	453	489	0.927	0.0000304	5127
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00053	0.00052	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.698
RVIS EVS: -1.46
RVIS percentile EVS: 3.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.344

Gene Damage Prediction

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