Is DNHD1 p.Leu1807= (c.5419C>T) pathogenic?

DNHD1 p.Leu1807= (c.5419C>T) is classified Likely benign in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Rare (popmax 0.518%, afr); Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Leu1807= (c.5419C>T)?

DNHD1 p.Leu1807= (c.5419C>T) is associated with DNHD1-related disorder (ClinVar).

How common is DNHD1 p.Leu1807= (c.5419C>T) in the general population?

DNHD1 p.Leu1807= (c.5419C>T) is rare (popmax 0.518%, afr) (gnomAD).

DNHD1 p.Leu1807=

c.5419C>T · rs188331831 · VCV3045979

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.518%, afr)

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 -0.49	GERP -3.5
Overall
CADD	1.276	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.518% African / African-American · 379/73,188 alleles

Filtering AF 0.475% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.458%

Overall 0.0264% 410/1,552,286 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.518%	193
Admixed American	0.0333%	3,001
Remaining individualsnot grpmax-eligible	0.0216%	4,636
Middle Eastern	0.0167%	5,996

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.Leu1807=
Coding: c.5419C>T
MANE Select: NM_144666
dbSNP: rs188331831
Type: single nucleotide variant
Location: chr11:6546358 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Residue 1807: a UniProt-annotated variant site (in spgf65)

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-leu1807 (accessed [today's date]).

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