IGDCC4
protein-codingimmunoglobulin superfamily DCC subclass member 4, the group of Fibronectin type III domain containing|I-set domain containing
Gene summary
Predicted to be involved in cell-cell adhesion. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.5 kbGenCC 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 IGDCC4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020962.3. 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 | 2 | 3 | 5 | |||
| missense | 223 | 9 | 232 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 227 | 12 | 0 | 239 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066013.1 | 20 | MANE Select | |
| Ensembl | ENSP00000319623.3 | 20 | MANE Select | |
| Ensembl | ENSP00000530304.1 | 20 | Standard | |
| Ensembl | ENSP00000530304.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000352385
- Coding exons
- 20
- Length
- 41609
- Individuals with no LoFs
- 125691
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 57
- Defined
- 125748
- p
- 0.000227
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.73 | 588 | 719 | 0.818 | 0.0000431 | 7886 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00051 | 0.00049 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00014 | 0.00013 | rare |
| South Asian | 0.00044 | 0.00042 | rare |
| Other | 0.0010 | 0.00098 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- LoFtool
- 0.666
- RVIS EVS
- 0.86
- RVIS percentile EVS
- 88.52
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.170
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |