PRICKLE2 p.Arg72Ter
c.214C>T · rs2077760949 · VCV1064439
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 8 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PRICKLE2
- Protein
- p.Arg72Ter
- Coding
- c.214C>T
- MANE Select
- NM_198859
- dbSNP
- rs2077760949
- Type
- single nucleotide variant
- Location
- chr3:64163060 (GRCh38)
- Gene constraint
- LOEUF 0.34 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.41
- Residue 72
- the pet domain
Similar variants
- PRICKLE2 p.Arg72Gln Uncertain significance ★ ⚠ same residue
- PRICKLE2 c.*4330A>T Uncertain significance ★★ same type
- PRICKLE2 p.Ala143Thr Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala146Val Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala149Ser Uncertain significance ★★ same type
- PRICKLE2 p.Ala309Gly Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala33Ser Uncertain significance ★★ ⚠ same type
- PRICKLE2 p.Ala548Thr 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/prickle2-p-arg72ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown