CHM p.Ser39fs
c.115dup · VCV3725069
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 8.2 | GERP 2.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CHM
- Protein
- p.Ser39fs
- Coding
- c.115dup
- MANE Select
- NM_000390
- Type
- Duplication
- Location
- chrX:86027491 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM p.Ser39Leu Uncertain significance ★★ ⚠ same residue
- CHM p.Asn283Ter Pathogenic ★★ same type
- CHM p.Asp353fs Pathogenic ★★ same type
- CHM p.Glu480fs Pathogenic ★★ same type
- CHM c.117-27_117-26dup Likely benign ★★ same type
- CHM c.117-27dup Benign ★★ same type
- CHM p.Asn644_Leu645insGlnSerThrAsn Benign/Likely benign ★★ same type
- CHM c.1609+2dup 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-ser39fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown