Is DAAM2 p.Ala869= (c.2607T>C) pathogenic?

DAAM2 p.Ala869= (c.2607T>C) is classified Benign in DAAM2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-17). Common (popmax 85.2%, eas) — too common for a highly-penetrant pathogenic allele; Associated with DAAM2-related disorder.

What condition is associated with DAAM2 p.Ala869= (c.2607T>C)?

DAAM2 p.Ala869= (c.2607T>C) is associated with DAAM2-related disorder (ClinVar).

DAAM2 p.Ala869=

Q: How common is DAAM2 p.Ala869= (c.2607T>C) in the general population?

DAAM2 p.Ala869= (c.2607T>C) is common (popmax 85.2%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2607T>C · rs3004067 · VCV3059909

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 85.2%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

DAAM2-related disorder

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 -10	GERP -5.3
Overall
CADD	1.402	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 85.2% East Asian · 38,159/44,806 alleles

Filtering AF 84.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 84.2%

Overall 63.3% 1,014,458/1,602,868 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	85.2%	1
African / African-American	78.2%	1
Amishnot grpmax-eligible	75.1%	1
South Asian	74.4%	1
Middle Eastern	73.2%	1
Ashkenazi Jewishnot grpmax-eligible	69.7%	1
Finnishnot grpmax-eligible	67%	1
Remaining individualsnot grpmax-eligible	66.1%	2
Admixed American	62.5%	2
European (non-Finnish)	60.1%	2

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.Ala869=
Coding: c.2607T>C
MANE Select: NM_001201427
dbSNP: rs3004067
Type: single nucleotide variant
Location: chr6:39897271 (GRCh38)
Gene constraint: LOEUF 0.488 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 80.02
Residue 869: 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

DAAM2-related disorder

Similar variants

DAAM2 p.Ala829Thr Uncertain significance ⚠ same condition
DAAM2 p.Glu997Lys Uncertain significance ⚠ same condition
DAAM2 p.Gly527Val Uncertain significance ⚠ same condition
DAAM2 c.1845+7A>G Likely benign same condition
DAAM2 c.2342-10C>T Likely benign same condition
DAAM2 c.2983-4G>A Likely benign same condition
DAAM2 c.2983-8G>C Likely benign same condition
DAAM2 p.Ala1054Thr Likely benign 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-ala869 (accessed [today's date]).

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