DYNC1H1 p.Pro2425=
c.7275G>A · rs141665695 · VCV472549
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0356%, nfe)
Conditions
2
Inborn genetic diseases
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 -15 | GERP -4.7 |
| Overall | ||
| CADD | 0.129 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0356%
European (non-Finnish) · 420/1,180,052 alleles
Filtering AF
0.0327%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0317%
Overall
0.0284%
458/1,614,092 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0356% | 2,810 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,905 |
| Finnishnot grpmax-eligible | 0.0203% | 4,924 |
| African / African-American | 0.00934% | 10,708 |
| Admixed American | 0.00167% | 60,002 |
| South Asian | 0.0011% | 91,084 |
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
- DYNC1H1
- Protein
- p.Pro2425=
- Coding
- c.7275G>A
- MANE Select
- NM_001376
- dbSNP
- rs141665695
- Type
- single nucleotide variant
- Location
- chr14:102015888 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Residue 2425
- an α-helix; the 'aaa 2' region
Similar variants
- DYNC1H1 p.Pro2425Gln Uncertain significance ★ ⚠ same residue
- DYNC1H1 p.Pro2425Leu 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
- DYNC1H1 p.Arg251Ser 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-pro2425 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown