ADD1 p.Pro15=
c.45G>T · rs140936293 · VCV790308
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.578%, mid)
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 -4.2 | GERP -3.8 |
| Overall | ||
| CADD | 4.824 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.578%
Middle Eastern · 35/6,056 alleles
Filtering AF
0.427%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.375%
Overall
0.0801%
1,292/1,613,398 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.578% | 173 |
| Admixed American | 0.34% | 294 |
| Remaining individualsnot grpmax-eligible | 0.238% | 419 |
| South Asian | 0.0935% | 1,069 |
| African / African-American | 0.0933% | 1,071 |
| European (non-Finnish) | 0.0615% | 1,625 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,959 |
| East Asian | 0.0201% | 4,984 |
| Finnishnot grpmax-eligible | 0.00625% | 16,003 |
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.Pro15=
- Coding
- c.45G>T
- MANE Select
- NM_001354761
- dbSNP
- rs140936293
- Type
- single nucleotide variant
- Location
- chr4:2875960 (GRCh38)
- Gene constraint
- LOEUF 0.387 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.73
- Residue 15
- the 'disordered' region
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-pro15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown