Is DYNC2H1 p.Asn2256= (c.6768C>T) pathogenic?

DYNC2H1 p.Asn2256= (c.6768C>T) is classified Likely benign in DYNC2H1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-27). Ultra-rare (popmax 0.0164%, mid); Associated with Jeune syndrome.

What condition is associated with DYNC2H1 p.Asn2256= (c.6768C>T)?

DYNC2H1 p.Asn2256= (c.6768C>T) is associated with Jeune syndrome (ClinVar).

How common is DYNC2H1 p.Asn2256= (c.6768C>T) in the general population?

DYNC2H1 p.Asn2256= (c.6768C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

DYNC2H1 p.Asn2256=

c.6768C>T · rs552515168 · VCV2895644

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

Jeune syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.67 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.47	GERP -3.5, phastCons 0.99
Overall
CADD	7.151	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,080 alleles

Filtering AF 0.00111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0009%

Overall 0.0018% 29/1,612,702 alleles · ultra-rare exomes 23/1,460,764 · genomes 6/151,938 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,080
African / African-American	0.00401%	24,935
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,560
South Asian	0.0022%	45,535
European (non-Finnish)	0.0017%	58,959
Admixed American	0.00167%	59,878
Finnishnot grpmax-eligible	0.00156%	63,972

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.Asn2256=
Coding: c.6768C>T
MANE Select: NM_001377
dbSNP: rs552515168
Type: single nucleotide variant
Location: chr11:103186376 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2256: a β-strand; the 'aaa 3' 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.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-asn2256 (accessed [today's date]).

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