Is DNAH1 p.Phe2044fs (c.6131del) pathogenic?

DNAH1 p.Phe2044fs (c.6131del) is classified Pathogenic in DNAH1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-02-09). Absent from gnomAD; Associated with spermatogenic failure 18.

What condition is associated with DNAH1 p.Phe2044fs (c.6131del)?

DNAH1 p.Phe2044fs (c.6131del) is associated with spermatogenic failure 18 (ClinVar).

How common is DNAH1 p.Phe2044fs (c.6131del) in the general population?

DNAH1 p.Phe2044fs (c.6131del) is absent from gnomAD (gnomAD).

DNAH1 p.Phe2044fs

c.6131del · rs1703258379 · VCV996332

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 38 of 78
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.1	GERP -3.8

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Phe2044fs
Coding: c.6131del
MANE Select: NM_015512
dbSNP: rs1703258379
Type: Deletion
Location: chr3:52370011 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Residue 2044: a UniProt-annotated variant site (in spgf18); the 'aaa 2' region

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

Similar variants

DNAH1 p.Phe2044= Likely benign ★ same residue
DNAH1 p.Ala4048fs Pathogenic/Likely pathogenic ★★ same condition
DNAH1 p.Asn648fs Pathogenic/Likely pathogenic ★★ same condition
DNAH1 p.Pro3909fs Pathogenic ★★ same condition
DNAH1 p.Val2559fs Pathogenic/Likely pathogenic ★★ same condition
DNAH1 c.6526-10_6526-9del Benign/Likely benign ★★ same condition
DNAH1 c.6666+14del Benign/Likely benign ★★ same condition
DNAH1 c.1435_1444+3del 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/dnah1-p-phe2044fs (accessed [today's date]).

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