HDDC2
protein-codingHD domain containing 2
Gene summary
Predicted to enable 5'-deoxynucleotidase activity. Predicted to be involved in deoxyribonucleoside monophosphate catabolic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- C6orf74
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~82.1 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 HDDC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016063.3. 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 | 1 | 1 | ||||
| missense | 33 | 3 | 36 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 37 | 3 | 0 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057147.2 | 6 | MANE Select | |
| Ensembl | ENSP00000381220.1 | 6 | MANE Select | |
| Ensembl | ENSP00000316242.9 | 3 | Standard | |
| Ensembl | ENSP00000477042.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- dUMP biosynthetic process
- pyrimidine deoxyribonucleotide salvage
- dephosphorylation
Molecular Function
- 5'-deoxynucleotidase activity
- protein binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000398153
- Coding exons
- 6
- Length
- 82175
- Individuals with no LoFs
- 124768
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 124794
- p
- 0.000104
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0891 | 112 | 115 | 0.977 | 0.00000602 | 1331 |
| Missense (PolyPhen) | 41 | 34.977 | 1.1722 | 392 | ||
| Synonymous | 0.364 | 38 | 41.0 | 0.928 | 0.00000212 | 385 |
| Loss of Function | 1.07 | 9 | 13.2 | 0.682 | 8.28e-7 | 130 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000093 | rare |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.610
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 36.86
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.257
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |