Is DOCK6 p.Arg1890His (c.5669G>A) pathogenic?

DOCK6 p.Arg1890His (c.5669G>A) is classified Uncertain significance in DOCK6 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-04-17). AlphaMissense: likely benign (0.0703); Ultra-rare (popmax 0.0117%, eas); Associated with Inborn genetic diseases.

What condition is associated with DOCK6 p.Arg1890His (c.5669G>A)?

DOCK6 p.Arg1890His (c.5669G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DOCK6 p.Arg1890His (c.5669G>A) in the general population?

DOCK6 p.Arg1890His (c.5669G>A) is ultra-rare (popmax 0.0117%, eas) (gnomAD).

What do computational predictors say about DOCK6 p.Arg1890His (c.5669G>A)?

AlphaMissense predicts likely benign (score 0.0703) — an in-silico prediction, not a clinical call.

DOCK6 p.Arg1890His

c.5669G>A · rs773454770 · VCV2144012

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0703 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0117%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0703	likely benign
REVEL	0.059	moderately benign-leaning
SaProt	LLR -9.99	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -2.5, phastCons 0.94
Regional constraint	o/e 0.92	unconstrained · MANE · 63 kb · p 1.8e-05 · regional, not allelic
Overall
CADD	26.8	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 0.0117% East Asian · 5/42,830 alleles

Filtering AF 0.00481% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00333%

Overall 0.00171% 27/1,578,436 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0117%	8,566
Admixed American	0.0112%	8,927
South Asian	0.00345%	28,957
African / African-American	0.00135%	73,992
European (non-Finnish)	0.00103%	96,878

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: DOCK6
Protein: p.Arg1890His
Coding: c.5669G>A
MANE Select: NM_020812
dbSNP: rs773454770
Type: single nucleotide variant
Location: chr19:11201908 (GRCh38)
Gene constraint: LOEUF 0.87 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.78 · 7 PDB
Residue 1890: the docker domain

Full DOCK6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DOCK6 p.Arg1890Cys Uncertain significance ★★ ⚠ same residue
DOCK6 c.5939+2T>C Pathogenic ★★ same condition
DOCK6 p.Glu1494Ter Pathogenic ★★ same condition
DOCK6 p.Ala1153Thr Uncertain significance ★★ ⚠ same condition
DOCK6 p.Ala1207Val Uncertain significance ★★ ⚠ same condition
DOCK6 p.Ala1241Thr Uncertain significance ★★ ⚠ same condition
DOCK6 p.Ala1319Val Uncertain significance ★★ ⚠ same condition
DOCK6 p.Ala133Thr 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/dock6-p-arg1890his (accessed [today's date]).

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