DYNC1H1 p.Phe3629=
c.10887C>T · rs141133453 · VCV198001
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 11 submitters
gnomAD v4.1
Rare
rare (popmax 0.231%, mid)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.421 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.49 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -5 | GERP -4.6 |
| Overall | ||
| CADD | 3.113 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.231%
Middle Eastern · 14/6,060 alleles
Filtering AF
0.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.112%
Overall
0.0229%
370/1,614,074 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.231% | 433 |
| South Asian | 0.0922% | 1,084 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,603 |
| Admixed American | 0.02% | 5,001 |
| European (non-Finnish) | 0.0187% | 5,339 |
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.Phe3629=
- Coding
- c.10887C>T
- MANE Select
- NM_001376
- dbSNP
- rs141133453
- Type
- single nucleotide variant
- Location
- chr14:102036621 (GRCh38)
- Gene constraint
- LOEUF 0.117 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Residue 3629
- the 'aaa 5' region; an α-helix
Similar variants
- DYNC1H1 p.Phe3629Leu Uncertain significance ★ 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
- DYNC1H1 p.Arg264Leu 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-phe3629 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown