CHM p.Ser495Ter
c.1484C>A · rs132630264 · VCV11149
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 15 |
| Splicing | ||
| SpliceAI | Δ0.59 | donor loss · deltas |
| Pangolin | Δ0.25 | loss · gain 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHM
- Protein
- p.Ser495Ter
- Coding
- c.1484C>A
- MANE Select
- NM_000390
- dbSNP
- rs132630264
- Type
- single nucleotide variant
- Location
- chrX:85894214 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM p.Ser495= Benign ★ 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.1244+1G>A Pathogenic ★★ same condition
- CHM c.1350-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHM c.1413+1G>T 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-ser495ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown