PTPRC p.Phe96=
c.288T>C · rs769834579 · VCV2738889
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
Conditions
1
immunodeficiency 104
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 -1.8 | GERP -3.5 |
| Overall | ||
| CADD | 0.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,870 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000186%
3/1,613,316 alleles · very rare
exomes 3/1,460,992 · genomes 0/152,324 · joint denominator
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
- PTPRC
- Protein
- p.Phe96=
- Coding
- c.288T>C
- MANE Select
- NM_002838
- dbSNP
- rs769834579
- Type
- single nucleotide variant
- Location
- chr1:198696899 (GRCh38)
- Gene constraint
- LOEUF 0.343 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.22 · 6 PDB
- Residue 96
- the 'disordered' region
Similar variants
- PTPRC p.Phe96Val Uncertain significance ★ ⚠ same residue
- PTPRC c.583+1G>A Likely pathogenic ★★ same condition
- PTPRC c.583+1G>T Likely pathogenic ★★ same condition
- PTPRC p.Arg890Ter Pathogenic/Likely pathogenic ★★ same condition
- PTPRC c.1830-3C>T Uncertain significance ★★ same condition
- PTPRC c.3509+5G>A Uncertain significance ★★ same condition
- PTPRC p.Ala113Ser Uncertain significance ★★ ⚠ same condition
- PTPRC p.Ala191Val Uncertain significance ★★ ⚠ 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/ptprc-p-phe96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown