SLC8A1 p.Phe817=
c.2451C>T · rs770080096 · VCV742964
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 8.7 | GERP 0.19, phastCons 1 |
| Overall | ||
| CADD | 12.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,084 alleles
Overall
0.000124%
2/1,614,192 alleles · very rare
exomes 2/1,461,862 · genomes 0/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,084 |
| European (non-Finnish) | 8.47e-05% | 1,180,032 |
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.Phe817=
- Coding
- c.2451C>T
- MANE Select
- NM_021097
- dbSNP
- rs770080096
- Type
- single nucleotide variant
- Location
- chr2:40139495 (GRCh38)
- Gene constraint
- LOEUF 0.363 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.64 · 5 PDB
- Residue 817
- an α-helix
Similar variants
- SLC8A1 p.Arg929= Benign ★★ same type
- 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
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-phe817 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown