Is DNAH11 p.Phe652= (c.1956C>T) pathogenic?

DNAH11 p.Phe652= (c.1956C>T) is classified Benign/Likely benign in DNAH11 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele; Associated with primary ciliary dyskinesia.

What condition is associated with DNAH11 p.Phe652= (c.1956C>T)?

DNAH11 p.Phe652= (c.1956C>T) is associated with primary ciliary dyskinesia, primary ciliary dyskinesia 7 (ClinVar).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DNAH11 p.Phe652=

Q: How common is DNAH11 p.Phe652= (c.1956C>T) in the general population?

DNAH11 p.Phe652= (c.1956C>T) is common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1956C>T · rs6963535 · VCV163097

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Common

common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

primary ciliary dyskinesia

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 -0.31	GERP -1.5
Overall
CADD	2.759	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 100% East Asian · 44,847/44,850 alleles

Filtering AF 99.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 98.9%

Overall 98.9% 1,595,515/1,613,386 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	100%	1
African / African-American	99.7%	1
Finnishnot grpmax-eligible	99.7%	1
Amishnot grpmax-eligible	99.6%	1
Admixed American	99.3%	1
Remaining individualsnot grpmax-eligible	98.8%	1
European (non-Finnish)	98.8%	1
Ashkenazi Jewishnot grpmax-eligible	98.7%	1
South Asian	98.3%	1
Middle Eastern	97.7%	1

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: DNAH11
Protein: p.Phe652=
Coding: c.1956C>T
MANE Select: NM_001277115
dbSNP: rs6963535
Type: single nucleotide variant
Location: chr7:21588619 (GRCh38)
Gene constraint: LOEUF 0.912 · pLI <0.01 (gnomAD)
Residue 652: the 'stem' region

Full DNAH11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: primary ciliary dyskinesia 7

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

DNAH11 c.10166-1G>C Likely pathogenic ★★ same condition
DNAH11 c.10569-2A>G Likely pathogenic ★★ same condition
DNAH11 c.10691+1G>T Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.10896+1G>T Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.11203-1G>C Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.11839+1G>A Pathogenic/Likely pathogenic ★★ same condition
DNAH11 c.11968-1G>C Pathogenic ★★ same condition
DNAH11 c.12934-1G>T Pathogenic/Likely pathogenic ★★ 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/dnah11-p-phe652 (accessed [today's date]).

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