SLMAP p.Ser417=
c.1251A>G · rs764903216 · VCV1733209
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.38 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 17.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,984 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00031%
5/1,613,058 alleles · very rare
exomes 5/1,460,754 · genomes 0/152,304 · joint denominator
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
- SLMAP
- Protein
- p.Ser417=
- Coding
- c.1251A>G
- MANE Select
- NM_001377540
- dbSNP
- rs764903216
- Type
- single nucleotide variant
- Location
- chr3:57871649 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.86 (gnomAD)
- Structure
- AlphaFold pLDDT 77.74 · 3 PDB
Similar variants
- SLMAP p.Ser417Ala Uncertain significance ★ ⚠ same residue
- SLMAP c.*38C>T Uncertain significance ★★ ⚠ same type
- SLMAP c.*55G>A Uncertain significance ★★ ⚠ same type
- SLMAP c.*70G>A Uncertain significance ★★ ⚠ same type
- SLMAP p.Ala365Asp Uncertain significance ★★ ⚠ same type
- SLMAP p.Ala506Ser Uncertain significance ★★ ⚠ same type
- SLMAP p.Ala597Val Uncertain significance ★★ ⚠ same type
- SLMAP p.Arg136Gln 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/slmap-p-ser417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown