Is DNAH1 p.Ser1929= (c.5787G>A) pathogenic?

DNAH1 p.Ser1929= (c.5787G>A) is classified Benign/Likely benign in DNAH1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-03). Common (popmax 8.16%, afr) — too common for a highly-penetrant pathogenic allele; Associated with spermatogenic failure 18.

What condition is associated with DNAH1 p.Ser1929= (c.5787G>A)?

DNAH1 p.Ser1929= (c.5787G>A) is associated with spermatogenic failure 18, ciliary dyskinesia, primary, 37 (ClinVar).

DNAH1 p.Ser1929=

Q: How common is DNAH1 p.Ser1929= (c.5787G>A) in the general population?

DNAH1 p.Ser1929= (c.5787G>A) is common (popmax 8.16%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.5787G>A · rs61738524 · VCV478466

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 8.16%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

spermatogenic failure 18

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 -0.55	GERP -2, phastCons 0.014
Overall
CADD	10.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.16% African / African-American · 6,118/75,000 alleles

Filtering AF 7.99% ClinGen BA1/BS1 input FAF95, joint · FAF99 7.92%

Overall 0.472% 7,613/1,613,754 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	8.16%	12
Admixed American	0.733%	136
Remaining individualsnot grpmax-eligible	0.724%	138
Middle Eastern	0.623%	161
Ashkenazi Jewishnot grpmax-eligible	0.108%	925
European (non-Finnish)	0.0436%	2,291
South Asian	0.0198%	5,059
East Asian	0.00223%	44,886

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: DNAH1
Protein: p.Ser1929=
Coding: c.5787G>A
MANE Select: NM_015512
dbSNP: rs61738524
Type: single nucleotide variant
Location: chr3:52368762 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Residue 1929: a UniProt-annotated variant site (in spgf18); the 'aaa 2' region

Full DNAH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spermatogenic failure 18 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ciliary dyskinesia, primary, 37

Similar variants

DNAH1 p.Ser1929Leu Uncertain significance ★★ ⚠ same residue
DNAH1 c.1034-2A>G Likely pathogenic ★★ same condition
DNAH1 c.10474+1G>A Pathogenic/Likely pathogenic ★★ same condition
DNAH1 c.10968+2C>T Likely pathogenic ★★ same condition
DNAH1 c.5244+1G>A Likely pathogenic ★★ same condition
DNAH1 p.Arg1702Ter Pathogenic ★★ same condition
DNAH1 p.Arg2479Ter Pathogenic/Likely pathogenic ★★ same condition
DNAH1 p.Arg2622Ter 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/dnah1-p-ser1929 (accessed [today's date]).

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