LYN p.Ile247=
c.741C>T · rs544863809 · VCV1674871
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.361%, 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 -1.2 | GERP -3.7, phastCons 0.001 |
| Overall | ||
| CADD | 4.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.361%
South Asian · 329/91,068 alleles
Filtering AF
0.329%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.316%
Overall
0.0264%
426/1,614,106 alleles · rare
exomes 401/1,461,866 · genomes 25/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.361% | 277 |
| Middle Eastern | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| European (non-Finnish) | 0.00669% | 14,937 |
| Admixed American | 0.00333% | 30,008 |
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.Ile247=
- Coding
- c.741C>T
- MANE Select
- NM_002350
- dbSNP
- rs544863809
- Type
- single nucleotide variant
- Location
- chr8:55953935 (GRCh38)
- Gene constraint
- LOEUF 0.282 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.44 · 6 PDB
- Residue 247
- the protein kinase domain; a β-strand
Similar variants
- 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
- LYN p.Val45Ile 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-ile247 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown