SAMD9 p.Ala438=
c.1314T>C · rs2535360765 · VCV2752743
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 0.88 | GERP 2.9, phastCons 0.96 |
| Overall | ||
| CADD | 8.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,044 alleles
Overall
0.000137%
2/1,461,458 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,044 |
| European (non-Finnish) | 8.48e-05% | 1,179,888 |
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
- SAMD9
- Protein
- p.Ala438=
- Coding
- c.1314T>C
- MANE Select
- NM_017654
- dbSNP
- rs2535360765
- Type
- single nucleotide variant
- Location
- chr7:93104784 (GRCh38)
- Gene constraint
- LOEUF 1.773 · pLI 0.03 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.79 · 10 PDB
Similar variants
- SAMD9 p.Ala438Pro Uncertain significance ★ ⚠ same residue
- SAMD9 p.Ala438Val Uncertain significance ★ ⚠ same residue
- SAMD9 p.Arg1293Trp Pathogenic ★★ ⚠ same type
- SAMD9 p.Arg459Gln Pathogenic ★★ ⚠ same type
- SAMD9 p.Arg685Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- SAMD9 p.Arg824Gln Pathogenic ★★ ⚠ same type
- SAMD9 p.Arg982Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- SAMD9 p.Arg982His Pathogenic/Likely pathogenic ★★ ⚠ 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/samd9-p-ala438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown