PCNT p.Arg3280Ter
c.9838A>T · VCV3673191
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 45 of 47 |
| Splicing | ||
| SpliceAI | Δ0.24 | donor loss · deltas |
| Pangolin | Δ0.38 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.2 | phastCons 1 |
| Overall | ||
| CADD | 47.0 | 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
- PCNT
- Protein
- p.Arg3280Ter
- Coding
- c.9838A>T
- MANE Select
- NM_006031
- Type
- single nucleotide variant
- Location
- chr21:46443947 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Residue 3280
- the 'disordered' region
Similar variants
- PCNT p.Arg3280Gly Uncertain significance ★ ⚠ same residue
- PCNT c.1032+1G>A Pathogenic/Likely pathogenic ★★ same type
- PCNT c.1680-1G>C Likely pathogenic ★★ same type
- PCNT c.3313-2A>C Likely pathogenic ★★ same type
- PCNT c.5995-2A>C Likely pathogenic ★★ same type
- PCNT c.7024+1G>A Likely pathogenic ★★ same type
- PCNT c.7024+1G>C Likely pathogenic ★★ same type
- PCNT c.7691-1G>A Likely pathogenic ★★ 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/pcnt-p-arg3280ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown