Is DYNC2H1 p.Val1771= (c.5313A>G) pathogenic?

DYNC2H1 p.Val1771= (c.5313A>G) is classified Benign/Likely benign in DYNC2H1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-29). Rare (popmax 0.81%, eas); Associated with Jeune syndrome.

What condition is associated with DYNC2H1 p.Val1771= (c.5313A>G)?

DYNC2H1 p.Val1771= (c.5313A>G) is associated with Jeune syndrome, asphyxiating thoracic dystrophy 3 (ClinVar).

How common is DYNC2H1 p.Val1771= (c.5313A>G) in the general population?

DYNC2H1 p.Val1771= (c.5313A>G) is rare (popmax 0.81%, eas) (gnomAD).

DYNC2H1 p.Val1771=

c.5313A>G · rs144553338 · VCV302043

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.81%, eas)

Conditions

Jeune syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.70	donor loss, 3 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -2.1	GERP -2.9
Overall
CADD	1.145	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.81% East Asian · 362/44,694 alleles

Filtering AF 0.741% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.714%

Overall 0.0235% 376/1,602,444 alleles · rare exomes 341/1,450,168 · genomes 35/152,276 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.81%	123
Remaining individualsnot grpmax-eligible	0.021%	4,765
Finnishnot grpmax-eligible	0.00158%	63,382

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.Val1771=
Coding: c.5313A>G
MANE Select: NM_001377
dbSNP: rs144553338
Type: single nucleotide variant
Location: chr11:103171047 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1771: a β-strand; the 'aaa 1' 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

Also linked: asphyxiating thoracic dystrophy 3

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.12156+1G>A Pathogenic/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-val1771 (accessed [today's date]).

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