CPTP p.Val153=
c.459C>T · rs140494438 · VCV2637999
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.413%, mid)
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 -5.1 | GERP -4.8 |
| Overall | ||
| CADD | 3.219 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.413%
Middle Eastern · 25/6,056 alleles
Filtering AF
0.287%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.254%
Overall
0.0637%
1,023/1,605,474 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.413% | 242 |
| African / African-American | 0.299% | 335 |
| Admixed American | 0.195% | 512 |
| Remaining individualsnot grpmax-eligible | 0.143% | 699 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0987% | 1,013 |
| European (non-Finnish) | 0.0451% | 2,216 |
| South Asian | 0.0111% | 9,034 |
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
- CPTP
- Protein
- p.Val153=
- Coding
- c.459C>T
- MANE Select
- NM_001029885
- dbSNP
- rs140494438
- Type
- single nucleotide variant
- Location
- chr1:1327577 (GRCh38)
- Gene constraint
- LOEUF 1.748 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.93 · 6 PDB
- Residue 153
- an α-helix
Similar variants
- CPTP p.Ala132Thr Uncertain significance ★ ⚠ same type
- CPTP p.Arg106Gln Uncertain significance ★ same type
- CPTP p.Arg106Gly Uncertain significance ★ ⚠ same type
- CPTP p.Arg106Trp Uncertain significance ★ ⚠ same type
- CPTP p.Arg110Cys Uncertain significance ★ same type
- CPTP p.Arg110His Uncertain significance ★ same type
- CPTP p.Arg126Cys Uncertain significance ★ ⚠ same type
- CPTP p.Arg133Cys 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/cptp-p-val153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown