DYNC1H1 p.Ala54=
c.162G>C · rs1322653837 · VCV2133708
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Charcot-Marie-Tooth disease axonal type 2O
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 1.4 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 13.6 | PHRED · no single calibrated threshold — expert panels disagree |
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
- DYNC1H1
- Protein
- p.Ala54=
- Coding
- c.162G>C
- MANE Select
- NM_001376
- dbSNP
- rs1322653837
- Type
- single nucleotide variant
- Location
- chr14:101964853 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Residue 54
- the 'stem' region; an α-helix
Disease context
Charcot-Marie-Tooth disease axonal type 2O — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal dominant Charcot-Marie-Tooth disease type 2O (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Childhood
- Prevalence
- <1 / 1 000 000 (Europe)
Similar variants
- DYNC1H1 p.Ala54Ser Uncertain significance ★ ⚠ same residue
- DYNC1H1 p.Ala54Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- DYNC1H1 p.Ala54Glu Likely benign ★ same residue
- DYNC1H1 p.Arg1567Gln Pathogenic/Likely pathogenic ★★ same condition
- DYNC1H1 p.Arg1623Gln Pathogenic/Likely pathogenic ★★ same condition
- DYNC1H1 p.Arg1962Cys Pathogenic ★★ same condition
- DYNC1H1 p.Arg1962His Likely pathogenic ★★ same condition
- DYNC1H1 p.Arg2332Cys Pathogenic/Likely 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/dync1h1-p-ala54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown