Is DNAH2 p.Phe3709= (c.11127T>C) pathogenic?

DNAH2 p.Phe3709= (c.11127T>C) is classified Likely benign in DNAH2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-30). Ultra-rare (popmax 0.0107%, afr); Associated with DNAH2-related disorder.

What condition is associated with DNAH2 p.Phe3709= (c.11127T>C)?

DNAH2 p.Phe3709= (c.11127T>C) is associated with DNAH2-related disorder (ClinVar).

How common is DNAH2 p.Phe3709= (c.11127T>C) in the general population?

DNAH2 p.Phe3709= (c.11127T>C) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

DNAH2 p.Phe3709=

c.11127T>C · rs781676620 · VCV3035349

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Conditions

DNAH2-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 -1	GERP -1.7, phastCons 0.004
Overall
CADD	2.25	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,896 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.000558% 9/1,613,232 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,362
Remaining individualsnot grpmax-eligible	0.0016%	62,440

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.Phe3709=
Coding: c.11127T>C
MANE Select: NM_020877
dbSNP: rs781676620
Type: single nucleotide variant
Location: chr17:7821354 (GRCh38)
Gene constraint: LOEUF 0.655 · pLI <0.01 (gnomAD)

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

Disease context

DNAH2-related disorder

Similar variants

DNAH2 p.Arg1633Gly Uncertain significance ⚠ same condition
DNAH2 c.11478+4G>A Benign same condition
DNAH2 c.1171-715G>A Likely benign same condition
DNAH2 c.1377-9C>A Likely benign same condition
DNAH2 c.1904+123T>C Benign same condition
DNAH2 c.1904+136C>T Likely benign same condition
DNAH2 c.1904+345A>G Likely benign same condition
DNAH2 c.3179+4C>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/dnah2-p-phe3709 (accessed [today's date]).

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