SAMD9 p.Ser623=
c.1869T>C · rs2535359640 · VCV2863400
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, 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 -0.59 | |
| Overall | ||
| CADD | 4.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,870 alleles
Overall
6.84e-05%
1/1,461,642 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
- SAMD9
- Protein
- p.Ser623=
- Coding
- c.1869T>C
- MANE Select
- NM_017654
- dbSNP
- rs2535359640
- Type
- single nucleotide variant
- Location
- chr7:93104229 (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.Ser623Phe Likely pathogenic ★ ⚠ same residue
- SAMD9 p.Ser623Pro Uncertain significance ★ ⚠ same residue
- SAMD9 p.Ser623Tyr 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
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-ser623 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown