Is DAAM2 p.Ser914= (c.2742C>T) pathogenic?

DAAM2 p.Ser914= (c.2742C>T) is classified Likely benign in DAAM2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-12-13). Rare (popmax 0.223%, sas); Associated with DAAM2-related disorder.

What condition is associated with DAAM2 p.Ser914= (c.2742C>T)?

DAAM2 p.Ser914= (c.2742C>T) is associated with DAAM2-related disorder (ClinVar).

How common is DAAM2 p.Ser914= (c.2742C>T) in the general population?

DAAM2 p.Ser914= (c.2742C>T) is rare (popmax 0.223%, sas) (gnomAD).

DAAM2 p.Ser914=

c.2742C>T · rs199848168 · VCV3048719

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.223%, sas)

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 -7.1	GERP -5.5
Overall
CADD	1.619	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.223% South Asian · 198/88,708 alleles

Filtering AF 0.198% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.188%

Overall 0.0154% 247/1,603,130 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.223%	448
East Asian	0.0204%	4,912
Remaining individualsnot grpmax-eligible	0.0113%	8,875
Admixed American	0.0034%	29,419
European (non-Finnish)	0.00264%	37,901

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.Ser914=
Coding: c.2742C>T
MANE Select: NM_001201427
dbSNP: rs199848168
Type: single nucleotide variant
Location: chr6:39900139 (GRCh38)
Gene constraint: LOEUF 0.488 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 80.02
Residue 914: 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-ser914 (accessed [today's date]).

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