ADD3 p.Phe49=
c.147C>T · rs1488644000 · VCV736783
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
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 4.1 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 13.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,798 alleles
Filtering AF
0.000555%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000806%
13/1,612,694 alleles · very rare
exomes 11/1,460,556 · genomes 2/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,899 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,428 |
| African / African-American | 0.00134% | 74,786 |
| European (non-Finnish) | 0.000763% | 131,054 |
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
- ADD3
- Protein
- p.Phe49=
- Coding
- c.147C>T
- MANE Select
- NM_016824
- dbSNP
- rs1488644000
- Type
- single nucleotide variant
- Location
- chr10:110100800 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.83
Similar variants
- ADD3 p.Gly367Asp Pathogenic/Likely pathogenic ★★ same type
- ADD3 c.1733-1G>A Uncertain significance ★★ same type
- ADD3 p.Ala588Gly Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg27Cys Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg46Gln Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg571His Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg645Gln Uncertain significance ★★ ⚠ same type
- ADD3 p.Asn312Asp 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/add3-p-phe49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown