SLC8A1 p.Arg929=
c.2785C>A · rs142336728 · VCV734794
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.229%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 10 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 10.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.229%
African / African-American · 172/75,026 alleles
Filtering AF
0.201%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.191%
Overall
0.0116%
188/1,614,114 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.229% | 436 |
| Admixed American | 0.0133% | 7,500 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,930 |
| European (non-Finnish) | 8.47e-05% | 1,180,018 |
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
- SLC8A1
- Protein
- p.Arg929=
- Coding
- c.2785C>A
- MANE Select
- NM_021097
- dbSNP
- rs142336728
- Type
- single nucleotide variant
- Location
- chr2:40115390 (GRCh38)
- Gene constraint
- LOEUF 0.363 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.64 · 5 PDB
Similar variants
- SLC8A1 p.Gly905= Benign ★★ same type
- SLC8A1 p.Ala307Val Uncertain significance ★ ⚠ same type
- SLC8A1 p.Ala322Val Uncertain significance ★ ⚠ same type
- SLC8A1 p.Ala349Gly Uncertain significance ★ ⚠ same type
- SLC8A1 p.Ala451Ser Uncertain significance ★ ⚠ same type
- SLC8A1 p.Ala504Gly Uncertain significance ★ ⚠ same type
- SLC8A1 p.Ala512Thr Uncertain significance ★ ⚠ same type
- SLC8A1 p.Ala537Ser 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/slc8a1-p-arg929 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown