PCNT p.Asp2047=
c.6141C>T · rs144445891 · VCV211870
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.111%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.60 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.2 | GERP -4.9 |
| Overall | ||
| CADD | 1.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
East Asian · 50/44,870 alleles
Filtering AF
0.0867%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0781%
Overall
0.00696%
112/1,608,382 alleles · rare
exomes 103/1,456,160 · genomes 9/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.111% | 897 |
| South Asian | 0.0264% | 3,795 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,205 |
| Middle Eastern | 0.0165% | 6,060 |
| Admixed American | 0.00667% | 15,001 |
| African / African-American | 0.00533% | 18,752 |
| European (non-Finnish) | 0.00144% | 69,404 |
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.Asp2047=
- Coding
- c.6141C>T
- MANE Select
- NM_006031
- dbSNP
- rs144445891
- Type
- single nucleotide variant
- Location
- chr21:46412983 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- 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
- PCNT c.8065-1G>C 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-asp2047 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown