Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 21.9%, eas) — too common for a highly-penetrant pathogenic allele
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.1 | GERP -5.1 |
| Overall | ||
| CADD | 0.238 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
21.9%
East Asian · 9,820/44,872 alleles
Filtering AF
21.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 21.4%
Overall
12.6%
202,726/1,613,908 alleles · common
exomes 184,748/1,461,640 · genomes 17,978/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 21.9% | 5 |
| Amishnot grpmax-eligible | 20.7% | 5 |
| South Asian | 20.2% | 5 |
| Middle Eastern | 16% | 6 |
| Admixed American | 15.9% | 6 |
| Finnishnot grpmax-eligible | 15.6% | 6 |
| Remaining individualsnot grpmax-eligible | 12.6% | 8 |
| European (non-Finnish) | 11.7% | 9 |
| Ashkenazi Jewishnot grpmax-eligible | 11.2% | 9 |
| African / African-American | 6.6% | 15 |
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.Ala2806=
- Coding
- c.8418G>A
- MANE Select
- NM_006031
- dbSNP
- rs9983522
- Type
- single nucleotide variant
- Location
- chr21:46431882 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- 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
- PCNT p.Arg1923Ter 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-ala2806 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown