CPD p.Arg460=
c.1380G>A · rs117331885 · VCV2647624
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.863%, nfe)
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 0.93 | GERP -3.4, phastCons 0.91 |
| Overall | ||
| CADD | 1.282 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.863%
European (non-Finnish) · 10,185/1,179,910 alleles
Filtering AF
0.849%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.843%
Overall
0.709%
11,445/1,613,858 alleles · rare
exomes 10,703/1,461,716 · genomes 742/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.863% | 116 |
| Remaining individualsnot grpmax-eligible | 0.632% | 158 |
| South Asian | 0.373% | 268 |
| Admixed American | 0.332% | 301 |
| Finnishnot grpmax-eligible | 0.214% | 467 |
| Ashkenazi Jewishnot grpmax-eligible | 0.206% | 485 |
| Middle Eastern | 0.198% | 505 |
| African / African-American | 0.155% | 646 |
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.Arg460=
- Coding
- c.1380G>A
- MANE Select
- NM_001304
- dbSNP
- rs117331885
- Type
- single nucleotide variant
- Location
- chr17:30422746 (GRCh38)
- Structure
- AlphaFold pLDDT 89.20
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-arg460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown