Is DYNC2I2 p.Ala5= (c.15G>A) pathogenic?

DYNC2I2 p.Ala5= (c.15G>A) is classified Likely benign in DYNC2I2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-23). Rare (popmax 0.453%, eas); Associated with short-rib thoracic dysplasia 11 with or without polydactyly.

What condition is associated with DYNC2I2 p.Ala5= (c.15G>A)?

DYNC2I2 p.Ala5= (c.15G>A) is associated with short-rib thoracic dysplasia 11 with or without polydactyly (ClinVar).

How common is DYNC2I2 p.Ala5= (c.15G>A) in the general population?

DYNC2I2 p.Ala5= (c.15G>A) is rare (popmax 0.453%, eas) (gnomAD).

DYNC2I2 p.Ala5=

c.15G>A · rs575543351 · VCV2060860

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.453%, eas)

Conditions

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 0.07	GERP -0.91
Overall
CADD	9.144	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.453% East Asian · 161/35,534 alleles

Filtering AF 0.396% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.374%

Overall 0.0114% 163/1,430,846 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.453%	221
Remaining individualsnot grpmax-eligible	0.00368%	27,167

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.Ala5=
Coding: c.15G>A
MANE Select: NM_052844
dbSNP: rs575543351
Type: single nucleotide variant
Location: chr9:128656712 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.66 · 4 PDB

Full DYNC2I2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

short-rib thoracic dysplasia 11 with or without polydactyly — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DYNC2I2 p.Ala5Gly Uncertain significance ★★ ⚠ same residue
DYNC2I2 p.Ala5Glu Uncertain significance ★ ⚠ same residue
DYNC2I2 p.Ala5Val Uncertain significance ★ ⚠ 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

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-ala5 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown