PTPRC p.Pro661=
c.1983G>A · rs748349607 · VCV1650620
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 -0.23 | GERP -4.5, phastCons 0.001 |
| Overall | ||
| CADD | 9.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,752 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.000745%
12/1,611,778 alleles · very rare
exomes 12/1,459,928 · genomes 0/151,850 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,752 |
| South Asian | 0.0011% | 91,030 |
| European (non-Finnish) | 0.000849% | 117,852 |
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.Pro661=
- Coding
- c.1983G>A
- MANE Select
- NM_002838
- dbSNP
- rs748349607
- Type
- single nucleotide variant
- Location
- chr1:198732308 (GRCh38)
- Gene constraint
- LOEUF 0.343 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.22 · 6 PDB
- Residue 661
- a UniProt-annotated variant site (in imd105); the tyrosine-protein phosphatase 1 domain
Similar variants
- 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
- PTPRC p.Ala60Thr 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-pro661 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown