Is DNAH7 p.Gly401Val (c.1202G>T) pathogenic?

DNAH7 p.Gly401Val (c.1202G>T) is classified Likely benign in DNAH7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-11-11). AlphaMissense: likely pathogenic (0.7659); Rare (popmax 0.556%, afr); Associated with DNAH7-related disorder.

What condition is associated with DNAH7 p.Gly401Val (c.1202G>T)?

DNAH7 p.Gly401Val (c.1202G>T) is associated with DNAH7-related disorder (ClinVar).

How common is DNAH7 p.Gly401Val (c.1202G>T) in the general population?

DNAH7 p.Gly401Val (c.1202G>T) is rare (popmax 0.556%, afr) (gnomAD).

What do computational predictors say about DNAH7 p.Gly401Val (c.1202G>T)?

AlphaMissense predicts likely pathogenic (score 0.7659) — an in-silico prediction, not a clinical call.

DNAH7 p.Gly401Val

c.1202G>T · rs114266575 · VCV3039954

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7659 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.556%, afr)

Conditions

DNAH7-related disorder

Computational evidence

Protein change
AlphaMissense	0.7659	likely pathogenic
REVEL	0.315	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.6, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 331 kb · p 0.14 · regional, not allelic
Overall
CADD	24.0	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 0.556% African / African-American · 408/73,394 alleles

Filtering AF 0.511% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.494%

Overall 0.034% 538/1,582,058 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.556%	180
Middle Eastern	0.17%	589
Admixed American	0.0634%	1,578
Remaining individualsnot grpmax-eligible	0.0623%	1,606
European (non-Finnish)	0.00394%	25,384
Ashkenazi Jewishnot grpmax-eligible	0.00355%	28,208
South Asian	0.00119%	83,912

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: DNAH7
Protein: p.Gly401Val
Coding: c.1202G>T
MANE Select: NM_018897
dbSNP: rs114266575
Type: single nucleotide variant
Location: chr2:196000855 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Residue 401: the 'stem' region

Full DNAH7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNAH7-related disorder

Similar variants

DNAH7 p.Glu3626= Uncertain significance ★ same condition
DNAH7 p.Val827Ile Uncertain significance ★ ⚠ same condition
DNAH7 p.Ala1739Thr Uncertain significance ⚠ same condition
DNAH7 p.Arg691Trp Uncertain significance ⚠ same condition
DNAH7 c.1173+4A>C Likely benign same condition
DNAH7 c.6118-10T>G Likely benign same condition
DNAH7 c.7507-6A>T Likely benign same condition
DNAH7 c.*9C>T 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/dnah7-p-gly401val (accessed [today's date]).

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