Is DNAH17 p.Val1602= (c.4806G>A) pathogenic?

DNAH17 p.Val1602= (c.4806G>A) is classified Likely benign in DNAH17 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-09). Ultra-rare (popmax 0.0933%, amr); Associated with DNAH17-related disorder.

What condition is associated with DNAH17 p.Val1602= (c.4806G>A)?

DNAH17 p.Val1602= (c.4806G>A) is associated with DNAH17-related disorder (ClinVar).

How common is DNAH17 p.Val1602= (c.4806G>A) in the general population?

DNAH17 p.Val1602= (c.4806G>A) is ultra-rare (popmax 0.0933%, amr) (gnomAD).

DNAH17 p.Val1602=

c.4806G>A · rs750525533 · VCV3035890

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0933%, amr)

Conditions

DNAH17-related disorder

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>A here scores Δ0.22 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.52	GERP -4
Overall
CADD	13.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0933% Admixed American · 56/60,004 alleles

Filtering AF 0.0737% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0667%

Overall 0.00347% 56/1,613,836 alleles · ultra-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.Val1602=
Coding: c.4806G>A
MANE Select: NM_173628
dbSNP: rs750525533
Type: single nucleotide variant
Location: chr17:78505443 (GRCh38)
Gene constraint: LOEUF 0.859 · pLI <0.01 (gnomAD)
Residue 1602: 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

DNAH17-related disorder

Similar variants

DNAH17 c.6818+1G>A Likely pathogenic same condition
DNAH17 p.Ala2154Thr Uncertain significance ⚠ same condition
DNAH17 c.10735-5T>G Likely benign same condition
DNAH17 c.11212-7C>T Likely benign same condition
DNAH17 c.11334+4C>T Likely benign same condition
DNAH17 c.11805+5G>A Likely benign same condition
DNAH17 c.12915+7G>T Benign same condition
DNAH17 c.1836-10C>G Likely benign 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-val1602 (accessed [today's date]).

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