Is DOCK9 p.Glu907= (c.2721G>A) pathogenic?

DOCK9 p.Glu907= (c.2721G>A) is classified Likely benign in DOCK9 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-09-11). Ultra-rare (popmax 0.076%, afr).

How common is DOCK9 p.Glu907= (c.2721G>A) in the general population?

DOCK9 p.Glu907= (c.2721G>A) is ultra-rare (popmax 0.076%, afr) (gnomAD).

DOCK9 p.Glu907=

c.2721G>A · rs372152944 · VCV751099

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.076%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1	GERP 0.7, phastCons 1
Overall
CADD	8.727	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.076% African / African-American · 57/74,970 alleles

Filtering AF 0.0602% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0545%

Overall 0.00379% 61/1,608,908 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.076%	1,315
Admixed American	0.00336%	29,725
Remaining individualsnot grpmax-eligible	0.00321%	31,186

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: DOCK9
Protein: p.Glu907=
Coding: c.2721G>A
MANE Select: NM_001366683
dbSNP: rs372152944
Type: single nucleotide variant
Location: chr13:98881582 (GRCh38)
Gene constraint: LOEUF 0.425 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.68 · 4 PDB

Full DOCK9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DOCK9 p.Ala434Val Benign ★★ same type
DOCK9 p.Asn1709= Benign ★★ same type
DOCK9 p.Cys2012= Benign/Likely benign ★★ same type
DOCK9 p.Leu1435= Benign ★★ same type
DOCK9 c.5023+908C>T Uncertain significance ★ ⚠ same type
DOCK9 c.5023+919C>T Uncertain significance ★ ⚠ same type
DOCK9 c.5023+952C>T Uncertain significance ★ ⚠ same type
DOCK9 c.5367+706T>A 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/dock9-p-glu907 (accessed [today's date]).

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