Is DYNC2I2 p.Gly36Val (c.107G>T) pathogenic?

DYNC2I2 p.Gly36Val (c.107G>T) is classified Likely benign in DYNC2I2 (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-22). AlphaMissense: likely benign (0.0977); Rare (popmax 0.467%, afr); Associated with short-rib thoracic dysplasia 11 with or without polydactyly.

What condition is associated with DYNC2I2 p.Gly36Val (c.107G>T)?

DYNC2I2 p.Gly36Val (c.107G>T) is associated with short-rib thoracic dysplasia 11 with or without polydactyly (ClinVar).

How common is DYNC2I2 p.Gly36Val (c.107G>T) in the general population?

DYNC2I2 p.Gly36Val (c.107G>T) is rare (popmax 0.467%, afr) (gnomAD).

What do computational predictors say about DYNC2I2 p.Gly36Val (c.107G>T)?

AlphaMissense predicts likely benign (score 0.0977) — an in-silico prediction, not a clinical call.

DYNC2I2 p.Gly36Val

c.107G>T · rs375929394 · VCV734463

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0977 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.467%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

short-rib thoracic dysplasia 11 with or without polydactyly

Computational evidence

Protein change
AlphaMissense	0.0977	likely benign
REVEL	0.235	benign-leaning
SaProt	LLR -6.90	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP -1, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 23 kb · p 0.59 · regional, not allelic
Overall
CADD	17.28	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.467% African / African-American · 323/69,230 alleles

Filtering AF 0.425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.408%

Overall 0.0305% 457/1,497,518 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.467%	214
Admixed American	0.0512%	1,953
Remaining individualsnot grpmax-eligible	0.0448%	2,234
Ashkenazi Jewishnot grpmax-eligible	0.0294%	3,407
European (non-Finnish)	0.00681%	14,691

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.Gly36Val
Coding: c.107G>T
MANE Select: NM_052844
dbSNP: rs375929394
Type: single nucleotide variant
Location: chr9:128656620 (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.Gly36= Likely benign ★ same residue
DYNC2I2 p.Gly36Leu Conflicting classifications of pathogenicity ★ same residue
DYNC2I2 p.Gly36Trp 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

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-gly36val (accessed [today's date]).

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