Is DNHD1 p.Gln3167= (c.9501G>A) pathogenic?

DNHD1 p.Gln3167= (c.9501G>A) is classified Benign in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-12-04). Common (popmax 19.3%, sas) — too common for a highly-penetrant pathogenic allele; Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Gln3167= (c.9501G>A)?

DNHD1 p.Gln3167= (c.9501G>A) is associated with DNHD1-related disorder (ClinVar).

DNHD1 p.Gln3167=

Q: How common is DNHD1 p.Gln3167= (c.9501G>A) in the general population?

DNHD1 p.Gln3167= (c.9501G>A) is common (popmax 19.3%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.9501G>A · rs72901756 · VCV3056797

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 19.3%, sas) — 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 1.9	GERP -0.2, phastCons 1
Overall
CADD	0.604	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 19.3% South Asian · 16,227/84,034 alleles

Filtering AF 19.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 19%

Overall 10.3% 160,138/1,551,352 alleles · common

Ancestry group	Frequency	1 in
South Asiangrpmax	19.3%	5
Middle Eastern	12.4%	8
Remaining individualsnot grpmax-eligible	10.8%	9
Ashkenazi Jewishnot grpmax-eligible	10.8%	9
European (non-Finnish)	10.7%	9
Admixed American	8.66%	12
Amishnot grpmax-eligible	8.22%	12
Finnishnot grpmax-eligible	3.95%	25
African / African-American	3.34%	30
East Asian	2.73%	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.Gln3167=
Coding: c.9501G>A
MANE Select: NM_144666
dbSNP: rs72901756
Type: single nucleotide variant
Location: chr11:6559265 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Residue 3167: 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-gln3167 (accessed [today's date]).

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