Is DYNC2I1 p.Asp931= (c.2793C>T) pathogenic?

DYNC2I1 p.Asp931= (c.2793C>T) is classified Benign/Likely benign in DYNC2I1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-18). Rare (popmax 0.375%, afr); Associated with short-rib thoracic dysplasia 8 with or without polydactyly.

What condition is associated with DYNC2I1 p.Asp931= (c.2793C>T)?

DYNC2I1 p.Asp931= (c.2793C>T) is associated with short-rib thoracic dysplasia 8 with or without polydactyly (ClinVar).

How common is DYNC2I1 p.Asp931= (c.2793C>T) in the general population?

DYNC2I1 p.Asp931= (c.2793C>T) is rare (popmax 0.375%, afr) (gnomAD).

DYNC2I1 p.Asp931=

c.2793C>T · rs199624775 · VCV707451

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.375%, afr)

Conditions

short-rib thoracic dysplasia 8 with or without polydactyly

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -6.8	GERP -4.2
Overall
CADD	0.261	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.375% African / African-American · 281/74,878 alleles

Filtering AF 0.339% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.325%

Overall 0.0263% 422/1,606,582 alleles · rare exomes 236/1,454,200 · genomes 186/152,382 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.375%	266
South Asian	0.0545%	1,836
Admixed American	0.0237%	4,212
Remaining individualsnot grpmax-eligible	0.0225%	4,447
East Asian	0.018%	5,569
European (non-Finnish)	0.00476%	21,009

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: DYNC2I1
Protein: p.Asp931=
Coding: c.2793C>T
MANE Select: NM_018051
dbSNP: rs199624775
Type: single nucleotide variant
Location: chr7:158941939 (GRCh38)
Gene constraint: LOEUF 0.802 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.87 · 4 PDB
Residue 931: a UniProt-annotated variant site (in srtd8; reduces interaction with ift proteins); a UniProt-annotated variant site (in srtd8)

Full DYNC2I1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

short-rib thoracic dysplasia 8 with or without polydactyly — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DYNC2I1 p.Arg228Ter Pathogenic/Likely pathogenic ★★ same condition
DYNC2I1 p.Arg441Ter Pathogenic/Likely pathogenic ★★ same condition
DYNC2I1 p.Arg642Ter Pathogenic/Likely pathogenic ★★ same condition
DYNC2I1 p.Arg762Ter Pathogenic ★★ same condition
DYNC2I1 p.Ala157Val Uncertain significance ★★ ⚠ same condition
DYNC2I1 p.Ala609Val Uncertain significance ★★ ⚠ same condition
DYNC2I1 p.Ala800Thr Uncertain significance ★★ ⚠ same condition
DYNC2I1 p.Ala822Thr 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/dync2i1-p-asp931 (accessed [today's date]).

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