PCNT p.Ala2965=
c.8895G>A · rs572222540 · VCV159680
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.8%, sas)
Conditions
1
microcephalic osteodysplastic primordial dwarfism type II
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 -10 | GERP -5.3 |
| Overall | ||
| CADD | 0.345 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.8%
South Asian · 1,640/91,084 alleles
Filtering AF
1.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.7%
Overall
0.109%
1,756/1,613,748 alleles · low-frequency
exomes 1,657/1,461,436 · genomes 99/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.8% | 56 |
| Remaining individualsnot grpmax-eligible | 0.117% | 856 |
| Middle Eastern | 0.033% | 3,031 |
| African / African-American | 0.00933% | 10,721 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,797 |
| East Asian | 0.00669% | 14,952 |
| Admixed American | 0.00333% | 30,016 |
| European (non-Finnish) | 0.00229% | 43,702 |
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.Ala2965=
- Coding
- c.8895G>A
- MANE Select
- NM_006031
- dbSNP
- rs572222540
- Type
- single nucleotide variant
- Location
- chr21:46436047 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- PCNT p.Ala2965Val Uncertain significance ★ ⚠ same residue
- PCNT c.1032+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PCNT c.1680-1G>C Likely pathogenic ★★ same condition
- PCNT c.5995-2A>C Likely pathogenic ★★ same condition
- PCNT c.7024+1G>C Likely pathogenic ★★ same condition
- PCNT c.7691-1G>A Likely pathogenic ★★ same condition
- PCNT c.9624-2A>G Likely pathogenic ★★ same condition
- PCNT p.Arg1730Ter Pathogenic/Likely pathogenic ★★ same condition
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-ala2965 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown