IGDCC3

Chr 15

immunoglobulin superfamily DCC subclass member 3

Also known as: HsT18880, PUNC

NCBI Gene: 9543 ENSG00000174498 UniProt: Q8IVU1

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]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.77

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.77LOEUF

pLI 0.000

Z-score 2.58

OE 0.50 (0.34–0.77)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.58Z-score

OE missense 0.93 (0.86–1.00)

453 obs / 488.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.50 (0.34–0.77)

0≤0.351.4

Missense OE?0.93 (0.86–1.00)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 16 / 31.7Missense obs/exp: 453 / 488.9Syn Z: 0.30

Background carrier burden — how many people carry a rare variant somewhere in IGDCC3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 44

1,120 rare PASS variants

Rare truncating (LoF)

1 in 1,000

157 rare PASS variants

Rare synonymous (reference)

1 in 70

507 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for IGDCC3. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 62	1 in 1,200
South Asian	~43k	1 in 43	1 in 490
Remaining (unassigned)	~30k	1 in 38	1 in 1,400
European (Finnish)	~27k	1 in 170	1 in 2,900
Admixed American	~22k	1 in 42	1 in 2,000
African / African American	~21k	1 in 48	1 in 1,300
East Asian	~20k	1 in 53	1 in 880
Ashkenazi Jewish	~13k	1 in 160	1 in 2,200
Middle Eastern	~2,884	1 in 64	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 13 of 14 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 14.? see exons ↓