CHM p.Ser453=
c.1359C>T · rs2148153518 · VCV1303896
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,185,907)
Conditions
1
choroideremia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.38 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.46 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP -0.5, phastCons 1 |
| Overall | ||
| CADD | 4.016 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,185,907). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CHM
- Protein
- p.Ser453=
- Coding
- c.1359C>T
- MANE Select
- NM_000390
- dbSNP
- rs2148153518
- Type
- single nucleotide variant
- Location
- chrX:85900700 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Disease context
choroideremia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Choroideremia (Orphanet):
- Inheritance
- X-linked recessive
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- CHM p.Ser453Ter Pathogenic same residue
- CHM c.116+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHM c.116+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CHM c.1166+1G>A Pathogenic ★★ same condition
- CHM c.1166+1G>C Pathogenic ★★ same condition
- CHM c.1350-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHM c.1413+1G>T Pathogenic ★★ same condition
- CHM c.1511-1G>A 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-ser453 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown