Is DYNC2H1 p.Val2242= (c.6726G>T) pathogenic?

DYNC2H1 p.Val2242= (c.6726G>T) is classified Likely benign in DYNC2H1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-28). Rare (popmax 0.132%, mid); Associated with Jeune syndrome.

What condition is associated with DYNC2H1 p.Val2242= (c.6726G>T)?

DYNC2H1 p.Val2242= (c.6726G>T) is associated with Jeune syndrome (ClinVar).

How common is DYNC2H1 p.Val2242= (c.6726G>T) in the general population?

DYNC2H1 p.Val2242= (c.6726G>T) is rare (popmax 0.132%, mid) (gnomAD).

DYNC2H1 p.Val2242=

c.6726G>T · rs200600809 · VCV695474

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.132%, mid)

Conditions

Jeune syndrome

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 0.16	GERP -2, phastCons 0.001
Overall
CADD	0.508	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.132% Middle Eastern · 8/6,078 alleles

Filtering AF 0.0655% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0477%

Overall 0.0143% 231/1,612,598 alleles · rare exomes 205/1,460,722 · genomes 26/151,876 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.132%	760
European (non-Finnish)	0.0165%	6,047
Remaining individualsnot grpmax-eligible	0.016%	6,240
Admixed American	0.015%	6,647
African / African-American	0.00668%	14,964
South Asian	0.00439%	22,764

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: DYNC2H1
Protein: p.Val2242=
Coding: c.6726G>T
MANE Select: NM_001377
dbSNP: rs200600809
Type: single nucleotide variant
Location: chr11:103186334 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

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.10042+2T>G Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 c.10462-2A>G Likely pathogenic ★★ same condition
DYNC2H1 c.10606-14A>G Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 c.10695+1G>A Likely pathogenic ★★ same condition
DYNC2H1 c.10813-2A>G Likely pathogenic ★★ same condition
DYNC2H1 c.11493+2T>A Likely pathogenic ★★ same condition
DYNC2H1 c.11650-1G>A Pathogenic/Likely pathogenic ★★ same condition
DYNC2H1 c.12457-1G>C Likely 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-val2242 (accessed [today's date]).

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