CHTF18 p.Pro123=
c.369C>G · rs373270981 · VCV2645864
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.221%, 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 -4.4 | GERP -4.2 |
| Overall | ||
| CADD | 0.334 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.221%
Middle Eastern · 13/5,886 alleles
Filtering AF
0.131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.104%
Overall
0.00239%
38/1,589,810 alleles · rare
exomes 35/1,437,572 · genomes 3/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.221% | 453 |
| South Asian | 0.0103% | 9,727 |
| Remaining individualsnot grpmax-eligible | 0.0065% | 15,377 |
| European (non-Finnish) | 0.00103% | 97,485 |
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
- CHTF18
- Protein
- p.Pro123=
- Coding
- c.369C>G
- MANE Select
- NM_022092
- dbSNP
- rs373270981
- Type
- single nucleotide variant
- Location
- chr16:789292 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.97 · 10 PDB
- Residue 123
- the 'disordered' region
Similar variants
- CHTF18 p.Ala770= Benign ★★ same type
- CHTF18 p.Arg804Cys Benign ★★ same type
- CHTF18 p.Asn820= Benign ★★ same type
- CHTF18 p.Asp284Glu Benign ★★ same type
- CHTF18 p.Glu233Lys Benign ★★ same type
- CHTF18 p.His179= Benign ★★ same type
- CHTF18 p.Leu541= Benign ★★ same type
- CHTF18 p.Leu797= 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/chtf18-p-pro123 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown