CHM p.Thr532=
c.1596T>A · rs2520027780 · VCV2995324
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000116%, 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 -3.5 | GERP -3.7 |
| Overall | ||
| CADD | 0.325 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000116%
European (non-Finnish) · 1/863,349 alleles
Overall
9.42e-05%
1/1,061,063 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.Thr532=
- Coding
- c.1596T>A
- MANE Select
- NM_000390
- dbSNP
- rs2520027780
- Type
- single nucleotide variant
- Location
- chrX:85878978 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM p.Thr532Asn Uncertain significance ★ ⚠ same residue
- 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
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-thr532 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown