Is DNAH9 p.Arg24fs (c.44_68dup) pathogenic?

DNAH9 p.Arg24fs (c.4468dup) is classified Benign/Likely benign in DNAH9 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-06-01). Low-frequency (popmax 2.75%, nfe).

How common is DNAH9 p.Arg24fs (c.44_68dup) in the general population?

DNAH9 p.Arg24fs (c.44_68dup) is low-frequency (popmax 2.75%, nfe) (gnomAD).

DNAH9 p.Arg24fs

c.44_68dup · rs761517350 · VCV774512

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

low-frequency (popmax 2.75%, nfe)

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 1 of 69
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.21	GERP -3.9
Overall
CADD	19.03	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.75% European (non-Finnish) · 29,902/1,086,766 alleles

Filtering AF 2.73% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.71%

Overall 2.53% 35,503/1,404,952 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	12.3%	8
Finnishnot grpmax-eligible	5.5%	18
European (non-Finnish)grpmax	2.75%	36
Remaining individualsnot grpmax-eligible	2.11%	47
Middle Eastern	1.69%	59
Admixed American	1.66%	60
South Asian	1.5%	67
Ashkenazi Jewishnot grpmax-eligible	1.07%	93
African / African-American	0.455%	220
East Asian	0.00603%	16,578

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DNAH9
Protein: p.Arg24fs
Coding: c.44_68dup
MANE Select: NM_001372
dbSNP: rs761517350
Type: Duplication
Location: chr17:11598539 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 24: the 'stem' region

Full DNAH9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DNAH9 p.Arg24Ter Pathogenic/Likely pathogenic ★★ same residue
DNAH9 p.Arg24Gly Uncertain significance ★★ same residue
DNAH9 p.Arg24= Likely benign ★★ same residue
DNAH9 p.Arg24Gln Uncertain significance ★ ⚠ same residue
DNAH9 p.Asp22fs Pathogenic ★★ same type
DNAH9 c.2596-2dup Uncertain significance ★★ same type
DNAH9 c.614+2dup Likely pathogenic ★ same type
DNAH9 p.Ala3288fs Pathogenic ★ same type

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/dnah9-p-arg24fs (accessed [today's date]).

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