LYN p.Pro52=
c.156T>C · rs769952180 · VCV1137924
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0209%, 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 1.4 | GERP 0.37, phastCons 1 |
| Overall | ||
| CADD | 9.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0209%
South Asian · 19/90,820 alleles
Filtering AF
0.0136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00137%
20/1,458,376 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0209% | 4,780 |
| European (non-Finnish) | 8.49e-05% | 1,177,740 |
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
- LYN
- Protein
- p.Pro52=
- Coding
- c.156T>C
- MANE Select
- NM_002350
- dbSNP
- rs769952180
- Type
- single nucleotide variant
- Location
- chr8:55946471 (GRCh38)
- Gene constraint
- LOEUF 0.282 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.44 · 6 PDB
- Residue 52
- the 'disordered' region
Similar variants
- LYN p.Pro52Arg Uncertain significance ★ ⚠ same residue
- LYN p.Ala150Thr Uncertain significance ★★ ⚠ same type
- LYN p.Ala70Thr Uncertain significance ★★ ⚠ same type
- LYN p.Arg360Trp Uncertain significance ★★ ⚠ same type
- LYN p.Glu47Asp Uncertain significance ★★ ⚠ same type
- LYN p.Ile227Val Uncertain significance ★★ ⚠ same type
- LYN p.Ser333Asn Uncertain significance ★★ same type
- LYN p.Thr30Ala 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/lyn-p-pro52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown