CHM p.Arg90=
c.270G>A · rs781060978 · VCV1588032
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00217%, amr)
Conditions
1
inherited retinal dystrophy
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 0.41 | GERP -0.98, phastCons 0.038 |
| Overall | ||
| CADD | 7.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/45,978 alleles
Overall
0.000183%
2/1,093,414 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00217% | 45,978 |
| European (non-Finnish) | 0.000112% | 891,949 |
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.Arg90=
- Coding
- c.270G>A
- MANE Select
- NM_000390
- dbSNP
- rs781060978
- Type
- single nucleotide variant
- Location
- chrX:85978811 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM c.116+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHM c.1244+1G>A Pathogenic ★★ same condition
- CHM c.189+1G>A Pathogenic ★★ same condition
- CHM c.49+5G>A Pathogenic/Likely pathogenic ★★ same condition
- CHM c.940+1G>A Pathogenic ★★ same condition
- CHM p.Arg239Ter Pathogenic ★★ same condition
- CHM p.Arg253Ter Pathogenic ★★ same condition
- CHM p.Arg267Ter Pathogenic ★★ same condition
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-arg90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown