CARTPT p.Val90=
c.270G>A · rs374875701 · VCV762928
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00195%, 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 2.8 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 4.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00195%
European (non-Finnish) · 23/1,179,734 alleles
Filtering AF
0.0013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00143%
23/1,613,016 alleles · very rare
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
- CARTPT
- Protein
- p.Val90=
- Coding
- c.270G>A
- MANE Select
- NM_004291
- dbSNP
- rs374875701
- Type
- single nucleotide variant
- Location
- chr5:71720534 (GRCh38)
- Gene constraint
- LOEUF 0.956 · pLI 0.13 (gnomAD)
- Structure
- AlphaFold pLDDT 73.81 · 1 PDB
- Residue 90
- a β-strand; a disulfide bond
Similar variants
- CARTPT p.Leu61Phe Uncertain significance ★★ ⚠ same type
- CARTPT c.159+172C>T Benign ★★ same type
- CARTPT c.160-204A>G Benign ★★ same type
- CARTPT c.*126C>A Benign ★★ same type
- CARTPT c.*39A>G Benign ★★ same type
- CARTPT c.*6C>G Benign ★★ same type
- CARTPT c.*77G>A Benign ★★ same type
- CARTPT p.Glu32Lys Likely benign ★★ ⚠ 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/cartpt-p-val90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown