DRAM2 p.Ser13=
c.39A>G · rs759095509 · VCV735837
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00364%, 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 -0.059 | GERP -3.9, phastCons 0.84 |
| Overall | ||
| CADD | 7.642 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00364%
European (non-Finnish) · 43/1,180,018 alleles
Filtering AF
0.00275%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.00301%
44/1,461,858 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00364% | 27,442 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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
- DRAM2
- Protein
- p.Ser13=
- Coding
- c.39A>G
- MANE Select
- NM_001349884
- dbSNP
- rs759095509
- Type
- single nucleotide variant
- Location
- chr1:111131516 (GRCh38)
- Gene constraint
- LOEUF 1.115 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.35
Similar variants
- DRAM2 c.340-2A>G Pathogenic/Likely pathogenic ★★ same type
- DRAM2 c.518-1G>A Likely pathogenic ★★ same type
- DRAM2 c.601-1G>A Likely pathogenic ★★ same type
- DRAM2 p.Gln147Ter Pathogenic/Likely pathogenic ★★ same type
- DRAM2 p.Trp165Ter Pathogenic ★★ same type
- DRAM2 c.199+6T>G Uncertain significance ★★ same type
- DRAM2 p.Ala39Thr Uncertain significance ★★ ⚠ same type
- DRAM2 p.Ala69Val 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/dram2-p-ser13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown