CPD p.Val677=
c.2031T>G · rs16965763 · VCV791199
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.825%, 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 0.08 | GERP -2.5, phastCons 0.97 |
| Overall | ||
| CADD | 5.381 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.825%
African / African-American · 618/74,940 alleles
Filtering AF
0.771%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.749%
Overall
0.0422%
680/1,610,888 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.825% | 121 |
| Admixed American | 0.0435% | 2,298 |
| Middle Eastern | 0.0331% | 3,024 |
| Remaining individualsnot grpmax-eligible | 0.0305% | 3,284 |
| European (non-Finnish) | 0.00119% | 84,131 |
| South Asian | 0.0011% | 90,732 |
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.Val677=
- Coding
- c.2031T>G
- MANE Select
- NM_004839 · reported on NM_001304
- dbSNP
- rs16965763
- Type
- single nucleotide variant
- Location
- chr17:30431785 (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-val677 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown