Is DNAH9 p.Val1459= (c.4377C>T) pathogenic?

DNAH9 p.Val1459= (c.4377C>T) is classified Benign/Likely benign in DNAH9 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-27). Rare (popmax 0.169%, nfe).

How common is DNAH9 p.Val1459= (c.4377C>T) in the general population?

DNAH9 p.Val1459= (c.4377C>T) is rare (popmax 0.169%, nfe) (gnomAD).

DNAH9 p.Val1459=

c.4377C>T · rs145085168 · VCV1654697

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.169%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.016	GERP -5.6, phastCons 0.48
Overall
CADD	0.111	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.169% European (non-Finnish) · 1,994/1,180,036 alleles

Filtering AF 0.163% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.16%

Overall 0.151% 2,434/1,614,216 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.787%	127
Amishnot grpmax-eligible	0.768%	130
Remaining individualsnot grpmax-eligible	0.197%	508
European (non-Finnish)grpmax	0.169%	592
Admixed American	0.045%	2,223
Finnishnot grpmax-eligible	0.0359%	2,784
African / African-American	0.0173%	5,773
Middle Eastern	0.0165%	6,062
South Asian	0.0143%	7,006

Ashkenazi Jewish 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.Val1459=
Coding: c.4377C>T
MANE Select: NM_001372
dbSNP: rs145085168
Type: single nucleotide variant
Location: chr17:11690199 (GRCh38)
Gene constraint: LOEUF 0.775 · pLI <0.01 (gnomAD)
Residue 1459: the 'stem' region; a UniProt-annotated variant site (in cild40)

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

Similar variants

DNAH9 c.11406+1G>T Likely pathogenic ★★ same type
DNAH9 c.1901+1G>A Likely pathogenic ★★ same type
DNAH9 c.2928+1G>A Likely pathogenic ★★ same type
DNAH9 c.5709+1G>T Likely pathogenic ★★ same type
DNAH9 c.615-2A>G Likely pathogenic ★★ same type
DNAH9 c.6847+1G>A Likely pathogenic ★★ same type
DNAH9 p.Arg1344Ter Pathogenic/Likely pathogenic ★★ same type
DNAH9 p.Arg1517Ter Pathogenic/Likely 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-val1459 (accessed [today's date]).

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