DAAM2 p.Phe17=
c.51C>T · rs376650953 · VCV3053048
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.36%, afr)
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 -4.8 |
| Overall | ||
| CADD | 6.272 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.36%
African / African-American · 993/72,866 alleles
Filtering AF
1.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
0.0727%
1,130/1,553,546 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.36% | 73 |
| Remaining individualsnot grpmax-eligible | 0.0913% | 1,096 |
| Admixed American | 0.081% | 1,235 |
| European (non-Finnish) | 0.00322% | 31,067 |
| East Asian | 0.00249% | 40,114 |
| South Asian | 0.00242% | 41,299 |
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.Phe17=
- Coding
- c.51C>T
- MANE Select
- NM_001201427
- dbSNP
- rs376650953
- Type
- single nucleotide variant
- Location
- chr6:39856353 (GRCh38)
- Gene constraint
- LOEUF 0.488 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 80.02
Similar variants
- 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
- MOCS1 c.*1909A>G Likely benign ★★ 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-phe17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown