PCNT p.Lys3010=
c.9030A>G · rs138791485 · VCV1336176
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, afr)
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 1.4 | GERP -5.4, phastCons 1 |
| Overall | ||
| CADD | 0.598 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
African / African-American · 23/74,958 alleles
Filtering AF
0.021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0178%
Overall
0.00161%
26/1,613,972 alleles · ultra-rare
exomes 10/1,461,708 · genomes 16/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0307% | 3,259 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
| Admixed American | 0.00167% | 60,016 |
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.Lys3010=
- Coding
- c.9030A>G
- MANE Select
- NM_006031
- dbSNP
- rs138791485
- Type
- single nucleotide variant
- Location
- chr21:46437012 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Residue 3010
- the 'interaction with nek2' region
Similar variants
- PCNT p.Lys3010Glu 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-lys3010 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown