LYN p.Ser205=
c.615C>T · rs147376208 · VCV1580229
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0476%, afr)
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 | GERP -3.5, phastCons 0.005 |
| Overall | ||
| CADD | 11.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0476%
African / African-American · 35/73,592 alleles
Filtering AF
0.0351%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0308%
Overall
0.00382%
61/1,594,902 alleles · ultra-rare
exomes 39/1,442,710 · genomes 22/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0476% | 2,103 |
| Remaining individualsnot grpmax-eligible | 0.0178% | 5,613 |
| Finnishnot grpmax-eligible | 0.00627% | 15,946 |
| Admixed American | 0.00372% | 26,907 |
| South Asian | 0.00344% | 29,033 |
| East Asian | 0.00225% | 44,398 |
| European (non-Finnish) | 0.000426% | 234,895 |
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.Ser205=
- Coding
- c.615C>T
- MANE Select
- NM_002350
- dbSNP
- rs147376208
- Type
- single nucleotide variant
- Location
- chr8:55952093 (GRCh38)
- Gene constraint
- LOEUF 0.282 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.44 · 6 PDB
- Residue 205
- the sh2 domain
Similar variants
- LYN p.Ser205Gly 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-ser205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown