DYNC2H1 p.Pro1220=
c.3660T>C · rs118191062 · VCV302028
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.57%, nfe)
Conditions
2
Jeune syndrome
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 -2.2 | GERP -4.7 |
| Overall | ||
| CADD | 4.709 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.57%
European (non-Finnish) · 30,255/1,179,012 alleles
Filtering AF
2.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.53%
Overall
2.15%
34,602/1,612,412 alleles · low-frequency
exomes 32,273/1,460,350 · genomes 2,329/152,062 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.57% | 39 |
| Finnishnot grpmax-eligible | 2.44% | 41 |
| Remaining individualsnot grpmax-eligible | 1.9% | 53 |
| Admixed American | 1.19% | 84 |
| Middle Eastern | 1.17% | 85 |
| Ashkenazi Jewishnot grpmax-eligible | 0.596% | 168 |
| South Asian | 0.407% | 246 |
| African / African-American | 0.359% | 279 |
| East Asian | 0.00893% | 11,198 |
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
- DYNC2H1
- Protein
- p.Pro1220=
- Coding
- c.3660T>C
- MANE Select
- NM_001377
- dbSNP
- rs118191062
- Type
- single nucleotide variant
- Location
- chr11:103155417 (GRCh38)
- Gene constraint
- LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1220
- the 'stem' region
Similar variants
- DYNC2H1 c.10042+2T>G Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.10462-2A>G Likely pathogenic ★★ same condition
- DYNC2H1 c.10606-14A>G Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.10695+1G>A Likely pathogenic ★★ same condition
- DYNC2H1 c.10813-2A>G Likely pathogenic ★★ same condition
- DYNC2H1 c.11493+2T>A Likely pathogenic ★★ same condition
- DYNC2H1 c.11650-1G>A Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.12156+1G>A 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/dync2h1-p-pro1220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown