Is DYNC2H1 p.Lys4205= (c.12615A>G) pathogenic?

DYNC2H1 p.Lys4205= (c.12615A>G) is classified Likely benign in DYNC2H1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-18). Very rare (popmax 0.00673%, amr); Associated with Jeune syndrome.

What condition is associated with DYNC2H1 p.Lys4205= (c.12615A>G)?

DYNC2H1 p.Lys4205= (c.12615A>G) is associated with Jeune syndrome (ClinVar).

How common is DYNC2H1 p.Lys4205= (c.12615A>G) in the general population?

DYNC2H1 p.Lys4205= (c.12615A>G) is very rare (popmax 0.00673%, amr) (gnomAD).

DYNC2H1 p.Lys4205=

c.12615A>G · rs1220607371 · VCV2729292

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00673%, amr)

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 1.6	GERP 1.8, phastCons 1
Overall
CADD	7.116	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00673% Admixed American · 4/59,424 alleles

Filtering AF 0.00227% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.000497% 8/1,608,334 alleles · very rare exomes 4/1,456,192 · genomes 4/152,142 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00673%	14,856
Remaining individualsnot grpmax-eligible	0.00482%	20,764
European (non-Finnish)	8.5e-05%	1,177,108

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.Lys4205=
Coding: c.12615A>G
MANE Select: NM_001377
dbSNP: rs1220607371
Type: single nucleotide variant
Location: chr11:103456323 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 4205: a β-strand

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-lys4205 (accessed [today's date]).

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