CSK p.Thr88=
c.264A>C · rs367837559 · VCV2645546
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, amr)
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 -3.6 | GERP -3.4 |
| Overall | ||
| CADD | 2.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
Admixed American · 15/59,982 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.0122%
197/1,610,726 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.025% | 3,999 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,927 |
| European (non-Finnish) | 0.0144% | 6,938 |
| Remaining individualsnot grpmax-eligible | 0.00803% | 12,453 |
| African / African-American | 0.00134% | 74,854 |
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
- CSK
- Protein
- p.Thr88=
- Coding
- c.264A>C
- MANE Select
- NM_004383
- dbSNP
- rs367837559
- Type
- single nucleotide variant
- Location
- chr15:74799293 (GRCh38)
- Gene constraint
- LOEUF 0.222 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.57 · 6 PDB
- Residue 88
- the sh2 domain
Similar variants
- CSK p.Gly287Asp Benign ★★ same type
- CSK p.Ala407Thr Uncertain significance ★ ⚠ same type
- CSK p.Arg56Cys Uncertain significance ★ ⚠ same type
- CSK p.Arg56His Uncertain significance ★ ⚠ same type
- CSK p.Arg94Gln Uncertain significance ★ ⚠ same type
- CSK p.Asn46Lys Uncertain significance ★ ⚠ same type
- CSK p.Asn63Ser Uncertain significance ★ ⚠ same type
- CSK p.Asp123Asn 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/csk-p-thr88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown