Is DNAH17 p.Ile1502fs (c.4502_4503dup) pathogenic?

DNAH17 p.Ile1502fs (c.45024503dup) is classified Likely pathogenic in DNAH17 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-10). Very rare (popmax 0.0011%, sas); Associated with spermatogenic failure 39.

What condition is associated with DNAH17 p.Ile1502fs (c.4502_4503dup)?

DNAH17 p.Ile1502fs (c.4502_4503dup) is associated with spermatogenic failure 39 (ClinVar).

How common is DNAH17 p.Ile1502fs (c.4502_4503dup) in the general population?

DNAH17 p.Ile1502fs (c.4502_4503dup) is very rare (popmax 0.0011%, sas) (gnomAD).

DNAH17 p.Ile1502fs

c.4502_4503dup · VCV3779266

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

spermatogenic failure 39

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 28 of 81
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 2.2, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,082 alleles

Overall 6.84e-05% 1/1,461,684 alleles · very rare

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: DNAH17
Protein: p.Ile1502fs
Coding: c.4502_4503dup
MANE Select: NM_173628
Type: Duplication
Location: chr17:78507538 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 (gnomAD)
Residue 1502: a UniProt-annotated variant site (in spgf39); the 'stem' region

Full DNAH17 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spermatogenic failure 39 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DNAH17 c.7752+2T>A Pathogenic/Likely pathogenic ★★ same condition
DNAH17 p.Ala1014Val Uncertain significance ★★ ⚠ same condition
DNAH17 p.Arg1217Thr Uncertain significance ★★ ⚠ same condition
DNAH17 p.Asn2661Ser Uncertain significance ★★ ⚠ same condition
DNAH17 p.Glu2382Gln Uncertain significance ★★ ⚠ same condition
DNAH17 p.Glu3698Lys Uncertain significance ★★ ⚠ same condition
DNAH17 p.Thr1705Met Uncertain significance ★★ same condition
DNAH17 p.Thr3735Met Uncertain significance ★★ ⚠ 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/dnah17-p-ile1502fs (accessed [today's date]).

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