ADD1 p.Ser12=
c.36A>C · rs1433130616 · VCV2583020
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, 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 5.9 | GERP -0.35, phastCons 1 |
| Overall | ||
| CADD | 12.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,036 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,460,140 alleles · very rare
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
- ADD1
- Protein
- p.Ser12=
- Coding
- c.36A>C
- MANE Select
- NM_001354761
- dbSNP
- rs1433130616
- Type
- single nucleotide variant
- Location
- chr4:2875951 (GRCh38)
- Gene constraint
- LOEUF 0.387 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.73
- Residue 12
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- ADD1 p.Val234= Benign ★★ same type
- ADD1 p.Val559Met Benign ★★ same type
- ADD1 c.2047+530G>A Uncertain significance ★ same type
- ADD1 c.2047+541G>T Uncertain significance ★ same type
- ADD1 p.Ala137Val Uncertain significance ★ ⚠ same type
- ADD1 p.Ala151Thr Uncertain significance ★ ⚠ same type
- ADD1 p.Ala156Thr Uncertain significance ★ ⚠ same type
- ADD1 p.Ala18Thr 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/add1-p-ser12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown