DYNC2I2 p.Pro7=
c.21G>A · rs771586181 · VCV2042425
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0135%, nfe)
Conditions
1
short-rib thoracic dysplasia 11 with or without polydactyly
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 -2.1 | GERP -4.5 |
| Overall | ||
| CADD | 4.962 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0135%
European (non-Finnish) · 149/1,104,276 alleles
Filtering AF
0.0117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.011%
Overall
0.0108%
155/1,436,390 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0135% | 7,411 |
| Remaining individualsnot grpmax-eligible | 0.00549% | 18,201 |
| African / African-American | 0.00297% | 33,655 |
| South Asian | 0.00149% | 67,254 |
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
- DYNC2I2
- Protein
- p.Pro7=
- Coding
- c.21G>A
- MANE Select
- NM_052844
- dbSNP
- rs771586181
- Type
- single nucleotide variant
- Location
- chr9:128656706 (GRCh38)
- Gene constraint
- LOEUF 1.036 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.66 · 4 PDB
Similar variants
- DYNC2I2 p.Pro7Ser Likely benign ★★ same residue
- DYNC2I2 c.1372+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DYNC2I2 p.Arg121Ter Pathogenic ★★ same condition
- DYNC2I2 p.Arg182Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DYNC2I2 p.Arg447Trp Pathogenic/Likely pathogenic ★★ same condition
- DYNC2I2 p.Ala131Val Uncertain significance ★★ ⚠ same condition
- DYNC2I2 p.Ala13Gly Uncertain significance ★★ ⚠ same condition
- DYNC2I2 p.Ala219Thr Uncertain significance ★★ ⚠ 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/dync2i2-p-pro7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown