PCNT p.Arg2892=
c.8676G>A · rs779468459 · VCV2974506
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0667%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.61 | GERP -1.5, phastCons 0.039 |
| Overall | ||
| CADD | 1.155 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0667%
Middle Eastern · 4/5,994 alleles
Filtering AF
0.0525%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0476%
Overall
0.00471%
76/1,613,924 alleles · ultra-rare
exomes 72/1,461,544 · genomes 4/152,380 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0667% | 1,499 |
| South Asian | 0.0659% | 1,518 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,498 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Finnishnot grpmax-eligible | 0.00157% | 63,850 |
| European (non-Finnish) | 0.000424% | 236,003 |
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
- PCNT
- Protein
- p.Arg2892=
- Coding
- c.8676G>A
- MANE Select
- NM_006031
- dbSNP
- rs779468459
- Type
- single nucleotide variant
- Location
- chr21:46432140 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Residue 2892
- the 'disordered' region
Similar variants
- PCNT p.Arg2892Lys 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-arg2892 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown