Is DNHD1 p.Glu845= (c.2535G>A) pathogenic?

DNHD1 p.Glu845= (c.2535G>A) is classified Likely benign in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-01). Rare (popmax 0.196%, eas); Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Glu845= (c.2535G>A)?

DNHD1 p.Glu845= (c.2535G>A) is associated with DNHD1-related disorder (ClinVar).

How common is DNHD1 p.Glu845= (c.2535G>A) in the general population?

DNHD1 p.Glu845= (c.2535G>A) is rare (popmax 0.196%, eas) (gnomAD).

DNHD1 p.Glu845=

c.2535G>A · rs181497792 · VCV3044653

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.196%, eas)

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 -0.14	GERP -4.4
Overall
CADD	1.388	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.196% East Asian · 80/40,896 alleles

Filtering AF 0.161% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.148%

Overall 0.00529% 82/1,551,158 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.196%	511
Remaining individualsnot grpmax-eligible	0.00166%	60,076
European (non-Finnish)	8.72e-05%	1,146,680

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.Glu845=
Coding: c.2535G>A
MANE Select: NM_144666
dbSNP: rs181497792
Type: single nucleotide variant
Location: chr11:6533710 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)

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-glu845 (accessed [today's date]).

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