Is DNHD1 p.Gln3520= (c.10560G>A) pathogenic?

DNHD1 p.Gln3520= (c.10560G>A) is classified Benign in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-11-12). Common (popmax 50.2%, afr) — too common for a highly-penetrant pathogenic allele; Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Gln3520= (c.10560G>A)?

DNHD1 p.Gln3520= (c.10560G>A) is associated with DNHD1-related disorder (ClinVar).

DNHD1 p.Gln3520=

Q: How common is DNHD1 p.Gln3520= (c.10560G>A) in the general population?

DNHD1 p.Gln3520= (c.10560G>A) is common (popmax 50.2%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.10560G>A · rs11825255 · VCV3055706

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 50.2%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

DNHD1-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 3.5	GERP 1.5, phastCons 1
Overall
CADD	0.822	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 50.2% African / African-American · 36,671/73,042 alleles

Filtering AF 49.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 49.6%

Overall 7.22% 112,046/1,551,534 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	50.2%	2
South Asian	11.2%	9
Admixed American	9.18%	11
Amishnot grpmax-eligible	8.88%	11
Middle Eastern	8.53%	12
Remaining individualsnot grpmax-eligible	8.26%	12
Ashkenazi Jewishnot grpmax-eligible	6.57%	15
Finnishnot grpmax-eligible	4.93%	20
European (non-Finnish)	4.34%	23
East Asian	2.68%	37

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: DNHD1
Protein: p.Gln3520=
Coding: c.10560G>A
MANE Select: NM_144666
dbSNP: rs11825255
Type: single nucleotide variant
Location: chr11:6564608 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Residue 3520: a UniProt-annotated variant site (in spgf65); a UniProt-annotated variant site (in spgf65; low expression, if any, in sperm flagella)

Full DNHD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DNHD1-related disorder

Similar variants

DNHD1 p.Glu4486Lys Uncertain significance ★★ ⚠ same condition
DNHD1 p.His4162Leu Uncertain significance ★★ ⚠ same condition
DNHD1 p.Arg2840Gln Uncertain significance ★ ⚠ same condition
DNHD1 p.Gln895Ter Conflicting classifications of pathogenicity ★ same condition
DNHD1 p.His3335Arg Uncertain significance ★ ⚠ same condition
DNHD1 p.Ala657Ser Uncertain significance ⚠ same condition
DNHD1 p.Glu971Lys Uncertain significance ⚠ same condition
DNHD1 p.Met1535Val Uncertain significance ⚠ 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/dnhd1-p-gln3520 (accessed [today's date]).

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