Is DYNC2I2 p.Thr291del (c.871_873del) pathogenic?

DYNC2I2 p.Thr291del (c.871873del) is classified Uncertain significance in DYNC2I2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-21). Very rare (popmax 0.00195%, nfe); Associated with short-rib thoracic dysplasia 11 with or without polydactyly.

What condition is associated with DYNC2I2 p.Thr291del (c.871_873del)?

DYNC2I2 p.Thr291del (c.871_873del) is associated with short-rib thoracic dysplasia 11 with or without polydactyly (ClinVar).

How common is DYNC2I2 p.Thr291del (c.871_873del) in the general population?

DYNC2I2 p.Thr291del (c.871_873del) is very rare (popmax 0.00195%, nfe) (gnomAD).

DYNC2I2 p.Thr291del

c.871_873del · rs775547736 · VCV2865959

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00195%, nfe)

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 · substitutions only
Constraint at this position
Conservation	phyloP 5.9	GERP 1.4, phastCons 1
Overall
CADD	16.14	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00195% European (non-Finnish) · 23/1,179,984 alleles

Filtering AF 0.0013% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00108%

Overall 0.00149% 24/1,613,316 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00195%	51,304
Remaining individualsnot grpmax-eligible	0.0016%	62,476

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.Thr291del
Coding: c.871_873del
MANE Select: NM_052844
dbSNP: rs775547736
Type: Deletion
Location: chr9:128635200 (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.Thr291= Benign ★★ same residue
DYNC2I2 p.Leu438fs Pathogenic/Likely pathogenic ★★ same condition
DYNC2I2 p.Phe439fs Pathogenic ★★ same condition
DYNC2I2 p.Pro210fs Pathogenic/Likely pathogenic ★★ same condition
DYNC2I2 p.Pro32fs Pathogenic/Likely pathogenic ★★ same condition
DYNC2I2 c.1372+5del Uncertain significance ★★ same condition
DYNC2I2 c.546-1_547del Likely pathogenic ★ same condition
DYNC2I2 p.Gln504_Gly505insTer 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/dync2i2-p-thr291del (accessed [today's date]).

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