Is DOCK5 p.Pro805Thr (c.2413C>A) pathogenic?

DOCK5 p.Pro805Thr (c.2413C>A) is classified Uncertain significance in DOCK5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-21). AlphaMissense: ambiguous (0.3972); Ultra-rare (popmax 0.0508%, afr).

How common is DOCK5 p.Pro805Thr (c.2413C>A) in the general population?

DOCK5 p.Pro805Thr (c.2413C>A) is ultra-rare (popmax 0.0508%, afr) (gnomAD).

What do computational predictors say about DOCK5 p.Pro805Thr (c.2413C>A)?

AlphaMissense predicts ambiguous (score 0.3972) — an in-silico prediction, not a clinical call.

DOCK5 p.Pro805Thr

c.2413C>A · rs369743990 · VCV2604655

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3972 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0508%, afr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3972	ambiguous
REVEL	0.149	moderately benign-leaning
SaProt	LLR -11.14	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.29 · evaluated, not missing
Constraint at this position
Conservation	phyloP 6	GERP 1.9, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 107 kb · p 5.5e-05 · regional, not allelic
Overall
CADD	23.0	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 0.0508% African / African-American · 38/74,864 alleles

Filtering AF 0.038% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0335%

Overall 0.00347% 56/1,612,656 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0508%	1,970
Remaining individualsnot grpmax-eligible	0.0208%	4,804
Middle Eastern	0.0164%	6,084
Admixed American	0.00167%	59,860
South Asian	0.0011%	90,694
European (non-Finnish)	0.00017%	589,710

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: DOCK5
Protein: p.Pro805Thr
Coding: c.2413C>A
MANE Select: NM_024940
dbSNP: rs369743990
Type: single nucleotide variant
Location: chr8:25340962 (GRCh38)
Gene constraint: LOEUF 0.679 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.63 · 11 PDB

Full DOCK5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DOCK5 c.4788+9C>T Benign ★★ same type
DOCK5 p.Leu986Phe Benign/Likely benign ★★ same type
DOCK5 p.Met987Leu Benign ★★ same type
DOCK5 p.Pro1467= Benign ★★ same type
DOCK5 p.Ser1306= Benign ★★ same type
DOCK5 p.Thr469Met Benign/Likely benign ★★ ⚠ same type
DOCK5 p.Ala1067Val Uncertain significance ★ ⚠ same type
DOCK5 p.Ala1194Ser 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/dock5-p-pro805thr (accessed [today's date]).

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