Is DAAM2 p.Glu894= (c.2682G>A) pathogenic?

DAAM2 p.Glu894= (c.2682G>A) is classified Likely benign in DAAM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-06). Ultra-rare (popmax 0.034%, eas); Associated with Inborn genetic diseases.

What condition is associated with DAAM2 p.Glu894= (c.2682G>A)?

DAAM2 p.Glu894= (c.2682G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DAAM2 p.Glu894= (c.2682G>A) in the general population?

DAAM2 p.Glu894= (c.2682G>A) is ultra-rare (popmax 0.034%, eas) (gnomAD).

DAAM2 p.Glu894=

c.2682G>A · rs750321033 · VCV3079864

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.034%, eas)

Conditions

Inborn genetic diseases

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 1.6	GERP -0.52, phastCons 1
Overall
CADD	11.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.034% East Asian · 15/44,116 alleles

Filtering AF 0.0209% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0169%

Overall 0.00137% 22/1,601,038 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.034%	2,941
Middle Eastern	0.0165%	6,050
European (non-Finnish)	0.000511%	195,656

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: DAAM2
Protein: p.Glu894=
Coding: c.2682G>A
MANE Select: NM_001201427
dbSNP: rs750321033
Type: single nucleotide variant
Location: chr6:39900079 (GRCh38)
Gene constraint: LOEUF 0.488 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 80.02
Residue 894: a UniProt-annotated variant site (in nphs24; affects the regulation of filopodia formation); the fh2 domain

Full DAAM2 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

DAAM2 p.Arg335Trp Uncertain significance ★★ ⚠ same condition
DAAM2 p.Arg676Trp Uncertain significance ★★ ⚠ same condition
DAAM2 p.Arg990Cys Uncertain significance ★★ ⚠ same condition
DAAM2 p.Gln760Arg Uncertain significance ★★ ⚠ same condition
DAAM2 p.Glu956Lys Uncertain significance ★★ ⚠ same condition
DAAM2 p.Ile699Val Uncertain significance ★★ ⚠ same condition
DAAM2 p.Ala117Val Uncertain significance ★ ⚠ same condition
DAAM2 p.Ala167Thr 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/daam2-p-glu894 (accessed [today's date]).

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