DYNC2I2 p.Phe388=
c.1164C>T · rs1860339417 · VCV1681198
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00899%, sas)
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 2.2 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 7.118 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00899%
South Asian · 8/89,002 alleles
Filtering AF
0.00446%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00318%
Overall
0.0005%
8/1,599,472 alleles · very rare
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.Phe388=
- Coding
- c.1164C>T
- MANE Select
- NM_052844
- dbSNP
- rs1860339417
- Type
- single nucleotide variant
- Location
- chr9:128634739 (GRCh38)
- Gene constraint
- LOEUF 1.036 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.66 · 4 PDB
Similar variants
- 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
- DYNC2I2 p.Ala369Val 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-phe388 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown