Is DNAH1 p.Trp2468fs (c.7402_7403del) pathogenic?

DNAH1 p.Trp2468fs (c.74027403del) is classified Pathogenic in DNAH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-21). Absent from gnomAD v4.1; Associated with spermatogenic failure 18.

What condition is associated with DNAH1 p.Trp2468fs (c.7402_7403del)?

DNAH1 p.Trp2468fs (c.7402_7403del) is associated with spermatogenic failure 18, ciliary dyskinesia, primary, 37 (ClinVar).

How common is DNAH1 p.Trp2468fs (c.7402_7403del) in the general population?

DNAH1 p.Trp2468fs (c.7402_7403del) is absent from gnomAD v4.1 (gnomAD).

DNAH1 p.Trp2468fs

c.7402_7403del · rs775289921 · VCV2951819

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,568,700)

Conditions

spermatogenic failure 18

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 48 of 78
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.82	GERP 2.1, phastCons 0.25

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,568,700). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DNAH1
Protein: p.Trp2468fs
Coding: c.7402_7403del
MANE Select: NM_015512
dbSNP: rs775289921
Type: Microsatellite
Location: chr3:52379927 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Residue 2468: a UniProt-annotated variant site (in spgf18)

Full DNAH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spermatogenic failure 18 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ciliary dyskinesia, primary, 37

Similar variants

DNAH1 p.Arg3490fs Pathogenic/Likely pathogenic ★★ same condition
DNAH1 c.3694-16CCCCT[3] Benign/Likely benign ★★ same condition
DNAH1 p.Ala1047fs Pathogenic ★ same condition
DNAH1 p.Ser2663fs Pathogenic ★ same condition
DNAH1 p.Val1761fs Pathogenic ★ same condition
DNAH1 c.9622-3_9622-2del Uncertain significance ★ same condition
DNAH1 p.1579PAG[1] Uncertain significance ★ same condition
DNAH1 p.Asn4069del Conflicting classifications of pathogenicity ★ 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/dnah1-p-trp2468fs (accessed [today's date]).

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