GHDC
protein-codingGH3 domain containing
Gene summary
Predicted to enable acid-amino acid ligase activity. Located in 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 ~5.7 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 GHDC variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032484.5. 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 | 3 | 1 | 4 | |||
| missense | 83 | 5 | 88 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 91 | 6 | 0 | 97 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115873.1 | 8 | MANE Select | |
| Ensembl | ENSP00000467585.1 | 8 | MANE Select | |
| RefSeq | NP_001136095.1 | 7 | Standard | |
| Ensembl | ENSP00000301671.7 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- biological_process
- neutrophil degranulation
Molecular Function
- molecular_function
Cellular Component
- extracellular region
- nuclear envelope
- endoplasmic reticulum
- membrane
- secretory granule lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301671
- Coding exons
- 8
- Length
- 5715
- Individuals with no LoFs
- 125644
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 104
- Defined
- 125748
- p
- 0.000414
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.884 | 251 | 294 | 0.855 | 0.0000175 | 3254 |
| Missense (PolyPhen) | 83 | 102.57 | 0.80924 | 1215 | ||
| Synonymous | 0.760 | 120 | 131 | 0.916 | 0.00000723 | 1223 |
| Loss of Function | 1.58 | 17 | 25.6 | 0.663 | 0.00000158 | 228 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0017 | 0.0017 | notable |
| Latino/Admixed American | 0.00042 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00042 | 0.00040 | rare |
| South Asian | 0.00025 | 0.00023 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- LoFtool
- 0.0798
- RVIS EVS
- 0.2
- RVIS percentile EVS
- 67.3
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0750
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |