Is DAAM2 p.Pro3= (c.9C>T) pathogenic?

DAAM2 p.Pro3= (c.9C>T) is classified Likely benign in DAAM2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-14). Rare (popmax 0.154%, afr); Associated with DAAM2-related disorder.

What condition is associated with DAAM2 p.Pro3= (c.9C>T)?

DAAM2 p.Pro3= (c.9C>T) is associated with DAAM2-related disorder (ClinVar).

How common is DAAM2 p.Pro3= (c.9C>T) in the general population?

DAAM2 p.Pro3= (c.9C>T) is rare (popmax 0.154%, afr) (gnomAD).

DAAM2 p.Pro3=

c.9C>T · VCV3352732

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.154%, afr)

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 0.86	GERP 1.2, phastCons 1
Overall
CADD	10.23	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.154% African / African-American · 111/72,182 alleles

Filtering AF 0.131% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.122%

Overall 0.0166% 255/1,534,890 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.154%	650
Middle Eastern	0.0694%	1,440
Admixed American	0.0444%	2,251
Remaining individualsnot grpmax-eligible	0.032%	3,128
Ashkenazi Jewishnot grpmax-eligible	0.0112%	8,903
European (non-Finnish)	0.00789%	12,676
South Asian	0.00632%	15,832
Finnishnot grpmax-eligible	0.00165%	60,632

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.Pro3=
Coding: c.9C>T
MANE Select: NM_001201427
Type: single nucleotide variant
Location: chr6:39856311 (GRCh38)
Gene constraint: LOEUF 0.488 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 80.02

Full DAAM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DAAM2-related disorder

Similar variants

DAAM2 p.Pro3Ser Likely benign ★ same residue
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

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-pro3 (accessed [today's date]).

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