Is DNAH7 p.Pro3563= (c.10689G>A) pathogenic?

DNAH7 p.Pro3563= (c.10689G>A) is classified Likely benign in DNAH7 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-11-11). Rare (popmax 0.528%, afr); Associated with DNAH7-related disorder.

What condition is associated with DNAH7 p.Pro3563= (c.10689G>A)?

DNAH7 p.Pro3563= (c.10689G>A) is associated with DNAH7-related disorder (ClinVar).

How common is DNAH7 p.Pro3563= (c.10689G>A) in the general population?

DNAH7 p.Pro3563= (c.10689G>A) is rare (popmax 0.528%, afr) (gnomAD).

DNAH7 p.Pro3563=

c.10689G>A · rs114520355 · VCV3040767

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.528%, afr)

Conditions

DNAH7-related disorder

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 -11	GERP -3.9
Overall
CADD	2.868	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.528% African / African-American · 396/75,026 alleles

Filtering AF 0.485% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.468%

Overall 0.0318% 514/1,614,096 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.528%	189
Middle Eastern	0.165%	606
Admixed American	0.055%	1,819
Remaining individualsnot grpmax-eligible	0.0448%	2,232
South Asian	0.00659%	15,180
East Asian	0.00446%	22,437
European (non-Finnish)	0.00331%	30,257

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.Pro3563=
Coding: c.10689G>A
MANE Select: NM_018897
dbSNP: rs114520355
Type: single nucleotide variant
Location: chr2:195794365 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Residue 3563: the 'aaa 6' 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-pro3563 (accessed [today's date]).

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