Is DNHD1 p.Arg4287Cys (c.12859C>T) pathogenic?

DNHD1 p.Arg4287Cys (c.12859C>T) is classified Uncertain significance in DNHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-13). AlphaMissense: likely benign (0.0848); Ultra-rare (popmax 0.0572%, amr).

How common is DNHD1 p.Arg4287Cys (c.12859C>T) in the general population?

DNHD1 p.Arg4287Cys (c.12859C>T) is ultra-rare (popmax 0.0572%, amr) (gnomAD).

What do computational predictors say about DNHD1 p.Arg4287Cys (c.12859C>T)?

AlphaMissense predicts likely benign (score 0.0848) — an in-silico prediction, not a clinical call.

DNHD1 p.Arg4287Cys

c.12859C>T · rs758714946 · VCV2522981

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0848 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0572%, amr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0848	likely benign
REVEL	0.078	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.53 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.055	GERP -0.7
Regional constraint	o/e 1.05	unconstrained · MANE · 3,234 bp · p 0.2 · regional, not allelic
Overall
CADD	21.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0572% Admixed American · 34/59,410 alleles

Filtering AF 0.042% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0369%

Overall 0.00535% 86/1,607,716 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0572%	1,747
Ashkenazi Jewishnot grpmax-eligible	0.0476%	2,100
Middle Eastern	0.0165%	6,050
Remaining individualsnot grpmax-eligible	0.0112%	8,895
African / African-American	0.0107%	9,348
East Asian	0.00674%	14,837
South Asian	0.00223%	44,755
European (non-Finnish)	0.00144%	69,262

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.Arg4287Cys
Coding: c.12859C>T
MANE Select: NM_144666
dbSNP: rs758714946
Type: single nucleotide variant
Location: chr11:6568862 (GRCh38)
Gene constraint: LOEUF 0.897 · pLI <0.01 (gnomAD)
Residue 4287: 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

Similar variants

DNHD1 p.Arg4287His Uncertain significance ★ ⚠ same residue
DNHD1 p.Arg2928Ter Pathogenic/Likely pathogenic ★★ same type
DNHD1 p.Arg3978Ter Pathogenic/Likely pathogenic ★★ same type
DNHD1 p.Arg4048Ter Pathogenic/Likely pathogenic ★★ same type
DNHD1 p.Glu1153Ter Pathogenic/Likely pathogenic ★★ same type
DNHD1 p.Tyr2166Ter Pathogenic/Likely pathogenic ★★ same type
DNHD1 p.Arg1582Trp Uncertain significance ★★ same type
DNHD1 p.Arg1873Ser Uncertain significance ★★ ⚠ same type

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-arg4287cys (accessed [today's date]).

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