Is DNHD1 p.Val3319= (c.9957G>C) pathogenic?

DNHD1 p.Val3319= (c.9957G>C) is classified Likely benign in DNHD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-12-02). Rare (popmax 0.224%, afr); Associated with DNHD1-related disorder.

What condition is associated with DNHD1 p.Val3319= (c.9957G>C)?

DNHD1 p.Val3319= (c.9957G>C) is associated with DNHD1-related disorder (ClinVar).

How common is DNHD1 p.Val3319= (c.9957G>C) in the general population?

DNHD1 p.Val3319= (c.9957G>C) is rare (popmax 0.224%, afr) (gnomAD).

DNHD1 p.Val3319=

c.9957G>C · rs138570572 · VCV3048158

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.224%, 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 -0.72	GERP -2.5
Overall
CADD	0.062	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.224% African / African-American · 164/73,190 alleles

Filtering AF 0.196% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.185%

Overall 0.0148% 230/1,551,660 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.224%	446
Admixed American	0.0451%	2,218
Remaining individualsnot grpmax-eligible	0.0349%	2,863
Middle Eastern	0.0167%	5,992
European (non-Finnish)	0.00183%	54,619

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.Val3319=
Coding: c.9957G>C
MANE Select: NM_144666
dbSNP: rs138570572
Type: single nucleotide variant
Location: chr11:6563797 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Residue 3319: 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-val3319 (accessed [today's date]).

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