PCNT p.Arg1942=
c.5826G>A · rs536281306 · VCV340510
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.3%, eas)
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 0.56 | GERP -5.1, phastCons 0.29 |
| Overall | ||
| CADD | 6.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.3%
East Asian · 569/43,892 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.17%
Overall
0.04%
632/1,581,796 alleles · low-frequency
exomes 586/1,429,450 · genomes 46/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.3% | 77 |
| Remaining individualsnot grpmax-eligible | 0.0357% | 2,798 |
| South Asian | 0.0325% | 3,076 |
| Middle Eastern | 0.02% | 5,008 |
| Admixed American | 0.00175% | 57,116 |
| European (non-Finnish) | 0.000853% | 117,180 |
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.Arg1942=
- Coding
- c.5826G>A
- MANE Select
- NM_006031
- dbSNP
- rs536281306
- Type
- single nucleotide variant
- Location
- chr21:46411899 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- PCNT p.Arg1942Gly 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-arg1942 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown