Is DAAM2 p.Pro3Ser (c.7C>T) pathogenic?

DAAM2 p.Pro3Ser (c.7C>T) is classified Likely benign in DAAM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-20). AlphaMissense: likely benign (0.1026); Rare (popmax 0.962%, sas); Associated with Inborn genetic diseases.

What condition is associated with DAAM2 p.Pro3Ser (c.7C>T)?

DAAM2 p.Pro3Ser (c.7C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DAAM2 p.Pro3Ser (c.7C>T) in the general population?

DAAM2 p.Pro3Ser (c.7C>T) is rare (popmax 0.962%, sas) (gnomAD).

What do computational predictors say about DAAM2 p.Pro3Ser (c.7C>T)?

AlphaMissense predicts likely benign (score 0.1026) — an in-silico prediction, not a clinical call.

DAAM2 p.Pro3Ser

c.7C>T · VCV3270755

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1026 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.962%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1026	likely benign
REVEL	0.4	indeterminate
SaProt	LLR -5.54	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP 1.3, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 8,771 bp · p 0.57 · regional, not allelic
Overall
CADD	17.89	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.962% South Asian · 758/78,804 alleles

Filtering AF 0.905% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.882%

Overall 0.0523% 802/1,532,524 alleles · rare exomes 746/1,380,190 · genomes 56/152,334 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.962%	104
Remaining individualsnot grpmax-eligible	0.0624%	1,604
African / African-American	0.00555%	18,024
East Asian	0.00252%	39,660
European (non-Finnish)	0.000175%	569,856

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.Pro3Ser
Coding: c.7C>T
MANE Select: NM_001201427
Type: single nucleotide variant
Location: chr6:39856309 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DAAM2 p.Pro3= Likely benign same residue
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

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-pro3ser (accessed [today's date]).

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