CPD p.Arg5=
c.13C>A · rs181199485 · VCV778687
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.56%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.46 | GERP -2.5, phastCons 0.041 |
| Overall | ||
| CADD | 0.779 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.56%
African / African-American · 1,090/69,944 alleles
Filtering AF
1.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.45%
Overall
0.077%
1,186/1,540,324 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.56% | 64 |
| Admixed American | 0.0725% | 1,379 |
| Remaining individualsnot grpmax-eligible | 0.0721% | 1,387 |
| Middle Eastern | 0.0194% | 5,152 |
| South Asian | 0.00118% | 84,858 |
| European (non-Finnish) | 0.00113% | 88,765 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CPD
- Protein
- p.Arg5=
- Coding
- c.13C>A
- MANE Select
- NM_004839 · reported on NM_001304
- dbSNP
- rs181199485
- Type
- single nucleotide variant
- Location
- chr17:30378993 (GRCh38)
- Structure
- AlphaFold pLDDT 89.20
- Residue 5
- the wh1 domain
Similar variants
- HOMER2 p.Arg208Cys Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg213Trp Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg215His Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg309Cys Uncertain significance ★★ ⚠ same type
- HOMER2 p.Arg334Gln Uncertain significance ★★ ⚠ same type
- HOMER2 p.Asn235Lys Uncertain significance ★★ ⚠ same type
- HOMER2 p.Glu255Asp Uncertain significance ★★ ⚠ same type
- HOMER2 p.Glu274Lys Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cpd-p-arg5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown