CHTF18 p.Lys324=
c.972G>A · rs151271197 · VCV775363
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.77%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.045 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP -0.37, phastCons 1 |
| Overall | ||
| CADD | 8.604 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.77%
Middle Eastern · 107/6,056 alleles
Filtering AF
1.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.39%
Overall
0.877%
14,134/1,611,012 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.77% | 57 |
| Finnishnot grpmax-eligible | 1.37% | 73 |
| Ashkenazi Jewishnot grpmax-eligible | 1.15% | 87 |
| South Asian | 1.11% | 90 |
| European (non-Finnish) | 0.927% | 108 |
| Remaining individualsnot grpmax-eligible | 0.887% | 113 |
| Admixed American | 0.372% | 269 |
| African / African-American | 0.148% | 676 |
| East Asian | 0.00223% | 44,818 |
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.Lys324=
- Coding
- c.972G>A
- MANE Select
- NM_022092
- dbSNP
- rs151271197
- Type
- single nucleotide variant
- Location
- chr16:791238 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.97 · 10 PDB
- Residue 324
- 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-lys324 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown