WDR49
protein-codingWD repeat domain 49, the group of WD repeat domain containing
Gene summary
This gene encodes a member of the WD repeat protein family with nine WD repeats. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~175.3 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 WDR49 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001366157.1. 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 | 2 | |||
| missense | 77 | 10 | 87 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 79 | 11 | 0 | 90 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001353086.1 | 18 | MANE Select | |
| Ensembl | ENSP00000507497.1 | 18 | MANE Select | |
| RefSeq | NP_001335880.1 | 18 | Standard | |
| RefSeq | NP_001335881.1 | 18 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000308378
- Coding exons
- 14
- Length
- 175300
- Individuals with no LoFs
- 125574
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 174
- Defined
- 125748
- p
- 0.000692
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.439 | 372 | 349 | 1.07 | 0.0000166 | 4617 |
| Missense (PolyPhen) | 90 | 69.971 | 1.2863 | 945 | ||
| Synonymous | 1.35 | 103 | 122 | 0.844 | 0.00000598 | 1251 |
| Loss of Function | 0.490 | 31 | 34.1 | 0.909 | 0.00000173 | 437 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0010 | 0.0010 | notable |
| Latino/Admixed American | 0.0010 | 0.00098 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0030 | 0.0030 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00043 | 0.00041 | rare |
| South Asian | 0.00041 | 0.00039 | rare |
| Other | 0.0016 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.974
- RVIS EVS
- 0.34
- RVIS percentile EVS
- 73.68
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.127
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |