RET p.Leu15=
c.43T>C · rs1418746925 · VCV1112203
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00285%, afr)
Conditions
2
hereditary neoplastic syndrome
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 0.48 | GERP -2.5, phastCons 0.99 |
| Overall | ||
| CADD | 9.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00285%
African / African-American · 2/70,232 alleles
Filtering AF
0.000473%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000177%
Overall
0.000132%
2/1,511,646 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
- RET
- Protein
- p.Leu15=
- Coding
- c.43T>C
- MANE Select
- NM_020975
- dbSNP
- rs1418746925
- Type
- single nucleotide variant
- Location
- chr10:43077301 (GRCh38)
- Gene constraint
- LOEUF 0.24 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.27 · 34 PDB
Similar variants
- RET p.Leu15Ser Uncertain significance ★ ⚠ same residue
- RET c.1759+1G>A Pathogenic/Likely pathogenic ★★ same condition
- RET c.1879+1G>A Pathogenic/Likely pathogenic ★★ same condition
- RET p.Arg180Ter Pathogenic ★★ same condition
- RET p.Arg77Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- RET p.Arg873Trp Likely pathogenic ★★ same condition
- RET p.Arg897Ter Pathogenic ★★ same condition
- RET p.Asp631Tyr Pathogenic ★★ ⚠ 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/ret-p-leu15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown