Is DYNC2H1 p.Thr697fs (c.2089del) pathogenic?

DYNC2H1 p.Thr697fs (c.2089del) is classified Pathogenic in DYNC2H1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-10). No gnomAD frequency available for this variant; Associated with Jeune syndrome.

What condition is associated with DYNC2H1 p.Thr697fs (c.2089del)?

DYNC2H1 p.Thr697fs (c.2089del) is associated with Jeune syndrome (ClinVar).

How common is DYNC2H1 p.Thr697fs (c.2089del) in the general population?

DYNC2H1 p.Thr697fs (c.2089del) is no gnomAD frequency available for this variant (gnomAD).

DYNC2H1 p.Thr697fs

c.2089del · rs2496903775 · VCV2838349

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Jeune syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 14 of 89
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.65	GERP -2.2, phastCons 0.017

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DYNC2H1
Protein: p.Thr697fs
Coding: c.2089del
MANE Select: NM_001377
dbSNP: rs2496903775
Type: Deletion
Location: chr11:103133690 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 697: the 'stem' region

Full DYNC2H1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Jeune syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DYNC2H1 c.1360+2del Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 p.Arg1881fs Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 p.Asn1495fs Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 p.Asp4156fs Pathogenic ★★ same condition
DYNC2H1 p.Gln1566fs Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 p.Glu1949fs Pathogenic ★★ same condition
DYNC2H1 p.His1896fs Pathogenic ★★ same condition
DYNC2H1 p.Ile4057fs 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/dync2h1-p-thr697fs (accessed [today's date]).

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