PYCR2 p.Asp64=
c.192C>T · rs149882706 · VCV748089
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0306%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.165 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -3.6 |
| Overall | ||
| CADD | 2.869 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0306%
African / African-American · 23/75,054 alleles
Filtering AF
0.0209%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0177%
Overall
0.00192%
31/1,614,178 alleles · ultra-rare
exomes 20/1,461,830 · genomes 11/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0306% | 3,263 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000169% | 590,016 |
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
- PYCR2
- Protein
- p.Asp64=
- Coding
- c.192C>T
- MANE Select
- NM_013328
- dbSNP
- rs149882706
- Type
- single nucleotide variant
- Location
- chr1:225922330 (GRCh38)
- Gene constraint
- LOEUF 1.029 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.60 · 2 PDB
- Residue 64
- a β-strand
Similar variants
- PYCR2 p.Arg119Cys Pathogenic/Likely pathogenic ★★ same type
- PYCR2 p.Arg119His Likely pathogenic ★★ same type
- PYCR2 p.Arg266Ter Pathogenic ★★ same type
- PYCR2 p.Gln226Ter Pathogenic/Likely pathogenic ★★ same type
- PYCR2 p.Ala187Thr Uncertain significance ★★ ⚠ same type
- PYCR2 p.Arg17Pro Uncertain significance ★★ ⚠ same type
- PYCR2 p.Arg200Cys Uncertain significance ★★ ⚠ same type
- PYCR2 p.Ile82Thr 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/pycr2-p-asp64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown