C3orf52
protein-codingchromosome 3 open reading frame 52, the group of MicroRNA protein coding host genes
Gene summary
Located in plasma membrane. Implicated in hypotrichosis 15. [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 ~44.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0859341
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0859341
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0859341
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Dermatologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to C3orf52 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024616.3. 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 | 0 | |||||
| missense | 2 | 1 | 3 | |||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 4 | 0 | 4 | 1 | 0 | 9 |
Highest pathogenic variant AF is 0.000009671043
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078892.3 | 6 | MANE Select | |
| Ensembl | ENSP00000264848.5 | 6 | MANE Select | |
| RefSeq | NP_001165218.1 | 4 | Standard | |
| Ensembl | ENSP00000399392.2 | 4 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000431717
- Coding exons
- 4
- Length
- 44670
- Individuals with no LoFs
- 124620
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 124631
- p
- 0.0000441
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.855 | 97 | 124 | 0.784 | 0.00000582 | 1612 |
| Missense (PolyPhen) | 23 | 24.157 | 0.95212 | 361 | ||
| Synonymous | 1.41 | 38 | 50.8 | 0.749 | 0.00000261 | 492 |
| Loss of Function | -0.0564 | 6 | 5.85 | 1.03 | 2.49e-7 | 80 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000070 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0631
Intolerance Scores
- LoFtool
- 0.868
- RVIS EVS
- 1.24
- RVIS percentile EVS
- 93.35
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |