Is DNAH2 p.Arg400His (c.1199G>A) pathogenic?

DNAH2 p.Arg400His (c.1199G>A) is classified Uncertain significance in DNAH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-04). AlphaMissense: likely pathogenic (0.8342); Very rare (popmax 0.00401%, afr); Associated with Inborn genetic diseases.

What condition is associated with DNAH2 p.Arg400His (c.1199G>A)?

DNAH2 p.Arg400His (c.1199G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DNAH2 p.Arg400His (c.1199G>A) in the general population?

DNAH2 p.Arg400His (c.1199G>A) is very rare (popmax 0.00401%, afr) (gnomAD).

What do computational predictors say about DNAH2 p.Arg400His (c.1199G>A)?

AlphaMissense predicts likely pathogenic (score 0.8342) — an in-silico prediction, not a clinical call.

DNAH2 p.Arg400His

c.1199G>A · rs145686578 · VCV2345926

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8342 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

Missense predictors

1/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8342	likely pathogenic
REVEL	0.253	benign-leaning
⇒ AlphaMissense calls this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 73 kb · p 9.6e-12 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,876 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00183%

Overall 0.00267% 43/1,613,384 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,959
South Asian	0.00329%	30,353
Remaining individualsnot grpmax-eligible	0.0032%	31,214
European (non-Finnish)	0.00288%	34,706
Finnishnot grpmax-eligible	0.00157%	63,816

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: DNAH2
Protein: p.Arg400His
Coding: c.1199G>A
MANE Select: NM_020877
dbSNP: rs145686578
Type: single nucleotide variant
Location: chr17:7739761 (GRCh38)
Gene constraint: LOEUF 0.655 · pLI <0.01 (gnomAD)
Residue 400: the 'stem' region

Full DNAH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DNAH2 p.Arg400Cys Uncertain significance ★ same residue
DNAH2 p.Arg400Leu Uncertain significance ★ same residue
DNAH2 p.Ala1036Val Uncertain significance ★★ ⚠ same condition
DNAH2 p.Arg1533Cys Uncertain significance ★★ ⚠ same condition
DNAH2 p.Arg2538Gln Uncertain significance ★★ same condition
DNAH2 p.Arg3759His Uncertain significance ★★ ⚠ same condition
DNAH2 p.Gln2069Glu Uncertain significance ★★ same condition
DNAH2 p.Ile4043Ser 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/dnah2-p-arg400his (accessed [today's date]).

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