CHPT1 p.Phe382=
c.1146C>T · rs116668070 · VCV780150
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.68%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.29 | donor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.549 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.68%
East Asian · 1,652/44,844 alleles
Filtering AF
3.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.48%
Overall
0.132%
2,125/1,612,924 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.68% | 27 |
| Remaining individualsnot grpmax-eligible | 0.527% | 190 |
| Ashkenazi Jewishnot grpmax-eligible | 0.135% | 740 |
| South Asian | 0.0538% | 1,858 |
| Middle Eastern | 0.033% | 3,030 |
| Admixed American | 0.025% | 3,999 |
| European (non-Finnish) | 0.00305% | 32,761 |
| Finnishnot grpmax-eligible | 0.00157% | 63,658 |
| African / African-American | 0.00133% | 74,976 |
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
- CHPT1
- Protein
- p.Phe382=
- Coding
- c.1146C>T
- MANE Select
- NM_020244
- dbSNP
- rs116668070
- Type
- single nucleotide variant
- Location
- chr12:101726374 (GRCh38)
- Gene constraint
- LOEUF 1.393 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.30 · 1 PDB
Similar variants
- CHPT1 p.Phe341Leu Benign ★★ ⚠ same type
- SYCP3 c.*205G>A Benign ★★ same type
- SYCP3 p.Gln222= Benign ★★ same type
- CHPT1 p.Ala147Ser Uncertain significance ★ same type
- CHPT1 p.Ala16Glu Uncertain significance ★ ⚠ same type
- CHPT1 p.Ala210Pro Uncertain significance ★ ⚠ same type
- CHPT1 p.Ala210Val Uncertain significance ★ ⚠ same type
- CHPT1 p.Ala3Val 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/chpt1-p-phe382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown