Is DYNC2H1 p.Asp1837= (c.5511C>T) pathogenic?

DYNC2H1 p.Asp1837= (c.5511C>T) is classified Conflicting classifications of pathogenicity in DYNC2H1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-10-09). Ultra-rare (popmax 0.0728%, nfe); Associated with asphyxiating thoracic dystrophy 3.

What condition is associated with DYNC2H1 p.Asp1837= (c.5511C>T)?

DYNC2H1 p.Asp1837= (c.5511C>T) is associated with asphyxiating thoracic dystrophy 3, Jeune syndrome (ClinVar).

How common is DYNC2H1 p.Asp1837= (c.5511C>T) in the general population?

DYNC2H1 p.Asp1837= (c.5511C>T) is ultra-rare (popmax 0.0728%, nfe) (gnomAD).

DYNC2H1 p.Asp1837=

c.5511C>T · rs201953670 · VCV302046

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0728%, nfe)

Conditions

asphyxiating thoracic dystrophy 3

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 0.7	GERP -3.9, phastCons 1
Overall
CADD	11.19	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0728% European (non-Finnish) · 852/1,170,744 alleles

Filtering AF 0.0686% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.067%

Overall 0.0575% 916/1,593,782 alleles · ultra-rare exomes 861/1,441,904 · genomes 55/151,878 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0728%	1,374
Remaining individualsnot grpmax-eligible	0.0455%	2,196
African / African-American	0.0232%	4,316
East Asian	0.0116%	8,607
South Asian	0.0102%	9,781
Finnishnot grpmax-eligible	0.00628%	15,914
Admixed American	0.00175%	57,298

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.Asp1837=
Coding: c.5511C>T
MANE Select: NM_001377
dbSNP: rs201953670
Type: single nucleotide variant
Location: chr11:103173258 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 1837: the 'aaa 1' region

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

Disease context

asphyxiating thoracic dystrophy 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Jeune syndrome

Similar variants

DYNC2H1 p.Asp1837Glu Uncertain significance ★ ⚠ same residue
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

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-asp1837 (accessed [today's date]).

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