CPNE5 p.Val236=
c.708G>A · rs35931885 · VCV773197
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.83%, 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 2.3 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 11.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.83%
African / African-American · 2,121/75,032 alleles
Filtering AF
2.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.69%
Overall
0.149%
2,405/1,614,166 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.83% | 35 |
| Admixed American | 0.257% | 390 |
| Remaining individualsnot grpmax-eligible | 0.162% | 619 |
| Middle Eastern | 0.148% | 674 |
| South Asian | 0.00439% | 22,771 |
| European (non-Finnish) | 0.00136% | 73,750 |
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
- CPNE5
- Protein
- p.Val236=
- Coding
- c.708G>A
- MANE Select
- NM_020939
- dbSNP
- rs35931885
- Type
- single nucleotide variant
- Location
- chr6:36774990 (GRCh38)
- Gene constraint
- LOEUF 0.695 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.40
- Residue 236
- the c2 2 domain
Similar variants
- CPNE5 p.Ala185Thr Uncertain significance ★ ⚠ same type
- CPNE5 p.Ala469Val Uncertain significance ★ ⚠ same type
- CPNE5 p.Ala515Asp Uncertain significance ★ ⚠ same type
- CPNE5 p.Ala8Pro Uncertain significance ★ ⚠ same type
- CPNE5 p.Arg129Cys Uncertain significance ★ ⚠ same type
- CPNE5 p.Arg257Gln Uncertain significance ★ same type
- CPNE5 p.Arg257Trp Uncertain significance ★ ⚠ same type
- CPNE5 p.Arg272Gln 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/cpne5-p-val236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown