CHM p.Ser563=
c.1689C>T · rs1264358219 · VCV1647305
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00297%, eas)
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 2.5 | GERP 0.19, phastCons 1 |
| Overall | ||
| CADD | 3.954 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00297%
East Asian · 1/33,695 alleles
Overall
9.16e-05%
1/1,091,989 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
- CHM
- Protein
- p.Ser563=
- Coding
- c.1689C>T
- MANE Select
- NM_000390
- dbSNP
- rs1264358219
- Type
- single nucleotide variant
- Location
- chrX:85873133 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM c.116+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHM c.116+1G>T Pathogenic/Likely pathogenic ★★ same type
- CHM c.1166+1G>A Pathogenic ★★ same type
- CHM c.1166+1G>C Pathogenic ★★ same type
- CHM c.1167-2A>G Pathogenic ★★ same type
- CHM c.1244+1G>A Pathogenic ★★ same type
- CHM c.1244+2T>A Pathogenic/Likely pathogenic ★★ same type
- CHM c.1349+1G>T Pathogenic/Likely pathogenic ★★ 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/chm-p-ser563 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown