Is DNAH1 p.Phe3601= (c.10803C>T) pathogenic?

DNAH1 p.Phe3601= (c.10803C>T) is classified Likely benign in DNAH1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-13). Ultra-rare (popmax 0.0527%, nfe); Associated with spermatogenic failure 18.

What condition is associated with DNAH1 p.Phe3601= (c.10803C>T)?

DNAH1 p.Phe3601= (c.10803C>T) is associated with spermatogenic failure 18, ciliary dyskinesia, primary, 37 (ClinVar).

How common is DNAH1 p.Phe3601= (c.10803C>T) in the general population?

DNAH1 p.Phe3601= (c.10803C>T) is ultra-rare (popmax 0.0527%, nfe) (gnomAD).

DNAH1 p.Phe3601=

c.10803C>T · rs373290672 · VCV478389

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0527%, nfe)

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 -4.4	GERP -3.2
Overall
CADD	5.114	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0527% European (non-Finnish) · 612/1,160,804 alleles

Filtering AF 0.0493% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0478%

Overall 0.0399% 631/1,580,970 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0527%	1,897
Middle Eastern	0.0339%	2,946
Remaining individualsnot grpmax-eligible	0.0098%	10,204
African / African-American	0.00535%	18,678
Admixed American	0.00513%	19,497
South Asian	0.00236%	42,304
East Asian	0.00224%	44,606
Finnishnot grpmax-eligible	0.0016%	62,560

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.Phe3601=
Coding: c.10803C>T
MANE Select: NM_015512
dbSNP: rs373290672
Type: single nucleotide variant
Location: chr3:52394641 (GRCh38)
Gene constraint: LOEUF 0.759 · pLI <0.01 (gnomAD)
Residue 3601: a UniProt-annotated variant site (in spgf18)

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 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
DNAH1 p.Arg2724Ter 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-phe3601 (accessed [today's date]).

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