Is DOCK6 p.Arg1173Trp (c.3517C>T) pathogenic?

DOCK6 p.Arg1173Trp (c.3517C>T) is classified Likely benign in DOCK6 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-01-28). AlphaMissense: likely benign (0.1984); Rare (popmax 0.841%, mid).

How common is DOCK6 p.Arg1173Trp (c.3517C>T) in the general population?

DOCK6 p.Arg1173Trp (c.3517C>T) is rare (popmax 0.841%, mid) (gnomAD).

What do computational predictors say about DOCK6 p.Arg1173Trp (c.3517C>T)?

AlphaMissense predicts likely benign (score 0.1984) — an in-silico prediction, not a clinical call.

DOCK6 p.Arg1173Trp

c.3517C>T · rs145081732 · VCV444446

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

AlphaMissense

likely benign

0.1984 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.841%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1984	likely benign
REVEL	0.128	moderately benign-leaning
SaProt	LLR -9.01	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 4.1	GERP -1.6, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 63 kb · p 1.8e-05 · regional, not allelic
Overall
CADD	27.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.841% Middle Eastern · 51/6,062 alleles

Filtering AF 0.657% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.592%

Overall 0.253% 4,080/1,613,782 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.841%	119
South Asian	0.34%	294
Ashkenazi Jewishnot grpmax-eligible	0.307%	325
European (non-Finnish)	0.277%	361
Remaining individualsnot grpmax-eligible	0.23%	434
African / African-American	0.159%	631
Admixed American	0.135%	741
Finnishnot grpmax-eligible	0.0172%	5,797
East Asian	0.00223%	44,890

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.Arg1173Trp
Coding: c.3517C>T
MANE Select: NM_020812
dbSNP: rs145081732
Type: single nucleotide variant
Location: chr19:11221884 (GRCh38)
Gene constraint: LOEUF 0.87 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.78 · 7 PDB

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

Similar variants

DOCK6 p.Arg1173Gln Uncertain significance ★★ ⚠ same residue
DOCK6 c.4491+1G>A Pathogenic ★★ same type
DOCK6 c.5939+2T>C Pathogenic ★★ same type
DOCK6 c.807-1G>A Likely pathogenic ★★ same type
DOCK6 p.Arg1526Ter Pathogenic/Likely pathogenic ★★ same type
DOCK6 p.Arg184Ter Pathogenic/Likely pathogenic ★★ same type
DOCK6 p.Arg488Ter Pathogenic/Likely pathogenic ★★ same type
DOCK6 p.Gln1188Ter Pathogenic/Likely pathogenic ★★ 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/dock6-p-arg1173trp (accessed [today's date]).

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