SAMD9 p.Cys835=
c.2505T>C · rs780680953 · VCV2443249
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00935%, afr)
Conditions
1
Inborn genetic diseases
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 -0.63 | |
| Overall | ||
| CADD | 1.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00935%
African / African-American · 7/74,848 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.000496%
8/1,613,338 alleles · very rare
exomes 3/1,461,242 · genomes 5/152,096 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00935% | 10,693 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,460 |
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.Cys835=
- Coding
- c.2505T>C
- MANE Select
- NM_017654
- dbSNP
- rs780680953
- Type
- single nucleotide variant
- Location
- chr7:93103593 (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.Cys835Arg Uncertain significance ★★ ⚠ same residue
- SAMD9 p.Ala1057Val Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1066Thr Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1069Thr Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1082Gly Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1102Asp Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala1195Asp Uncertain significance ★★ ⚠ same condition
- SAMD9 p.Ala123Ser Uncertain significance ★★ ⚠ same condition
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-cys835 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown