Is DOCK1 p.Val1503Phe (c.4507G>T) pathogenic?

DOCK1 p.Val1503Phe (c.4507G>T) is classified Uncertain significance in DOCK1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-09). AlphaMissense: likely benign (0.1282); Rare (popmax 0.142%, amr).

How common is DOCK1 p.Val1503Phe (c.4507G>T) in the general population?

DOCK1 p.Val1503Phe (c.4507G>T) is rare (popmax 0.142%, amr) (gnomAD).

What do computational predictors say about DOCK1 p.Val1503Phe (c.4507G>T)?

AlphaMissense predicts likely benign (score 0.1282) — an in-silico prediction, not a clinical call.

DOCK1 p.Val1503Phe

c.4507G>T · VCV3504332

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1282 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.142%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1282	likely benign
REVEL	0.137	moderately benign-leaning
SaProt	LLR -9.09	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 6.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.55	unconstrained · MANE · 4,483 bp · p 5.6e-06 · regional, not allelic
Overall
CADD	23.5	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM V1482F vs ClinVar V1503F) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.142% Admixed American · 85/59,938 alleles

Filtering AF 0.117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.108%

Overall 0.00546% 88/1,613,176 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.142%	705
East Asian	0.00223%	44,896
Remaining individualsnot grpmax-eligible	0.0016%	62,446
European (non-Finnish)	8.48e-05%	1,179,558

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: DOCK1
Protein: p.Val1503Phe
Coding: c.4507G>T
MANE Select: NM_001290223
Type: single nucleotide variant
Location: chr10:127415230 (GRCh38)
Gene constraint: LOEUF 0.637 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.63 · 1 PDB
Residue 1503: the docker domain

Full DOCK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DOCK1 p.Pro1783Ser Uncertain significance ★★ ⚠ same type
DOCK1 p.Ala1185Thr Uncertain significance ★ ⚠ same type
DOCK1 p.Ala151Thr Uncertain significance ★ ⚠ same type
DOCK1 p.Ala1578Ser Uncertain significance ★ ⚠ same type
DOCK1 p.Ala1590Gly Uncertain significance ★ ⚠ same type
DOCK1 p.Ala1620Val Uncertain significance ★ ⚠ same type
DOCK1 p.Ala1689Ser Uncertain significance ★ ⚠ same type
DOCK1 p.Ala280Thr 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/dock1-p-val1503phe (accessed [today's date]).

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