DAAM2 p.Arg886=
c.2658G>A · rs61748651 · VCV2656536
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0438%, nfe)
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 2.1 | GERP -4.3, phastCons 1 |
| Overall | ||
| CADD | 9.039 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0438%
European (non-Finnish) · 516/1,179,400 alleles
Filtering AF
0.0406%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0394%
Overall
0.0336%
541/1,612,394 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0438% | 2,286 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,459 |
| South Asian | 0.00552% | 18,102 |
| African / African-American | 0.00534% | 18,718 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,556 |
| Finnishnot grpmax-eligible | 0.00156% | 63,956 |
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.Arg886=
- Coding
- c.2658G>A
- MANE Select
- NM_001201427
- dbSNP
- rs61748651
- Type
- single nucleotide variant
- Location
- chr6:39898916 (GRCh38)
- Gene constraint
- LOEUF 0.488 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 80.02
- Residue 886
- a UniProt-annotated variant site (in nphs24; affects the regulation of filopodia formation); the fh2 domain
Similar variants
- DAAM2 p.Arg886Ser Uncertain significance ★ ⚠ same residue
- DAAM2 p.Arg335Trp Uncertain significance ★★ ⚠ same type
- DAAM2 p.Arg676Trp Uncertain significance ★★ ⚠ same type
- DAAM2 p.Arg990Cys Uncertain significance ★★ ⚠ same type
- DAAM2 p.Gln760Arg Uncertain significance ★★ ⚠ same type
- DAAM2 p.Glu956Lys Uncertain significance ★★ ⚠ same type
- DAAM2 p.Ile699Val Uncertain significance ★★ ⚠ same type
- DAAM2 p.Pro74Thr Uncertain significance ★★ ⚠ same type
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-arg886 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown