PCNT p.Ser1113=
c.3339T>C · rs61735805 · VCV159585
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.78%, nfe)
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 -2 | GERP -1.1 |
| Overall | ||
| CADD | 0.665 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.78%
European (non-Finnish) · 56,444/1,179,976 alleles
Filtering AF
4.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.74%
Overall
4.2%
67,821/1,614,146 alleles · low-frequency
exomes 63,162/1,461,834 · genomes 4,659/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 4.78% | 21 |
| Ashkenazi Jewishnot grpmax-eligible | 4.45% | 22 |
| Amishnot grpmax-eligible | 4.06% | 25 |
| Remaining individualsnot grpmax-eligible | 3.94% | 25 |
| Finnishnot grpmax-eligible | 3.9% | 26 |
| Middle Eastern | 3.73% | 27 |
| South Asian | 3.37% | 30 |
| Admixed American | 2.01% | 50 |
| African / African-American | 0.702% | 142 |
| East Asian | 0.0802% | 1,247 |
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.Ser1113=
- Coding
- c.3339T>C
- MANE Select
- NM_006031
- dbSNP
- rs61735805
- Type
- single nucleotide variant
- Location
- chr21:46385858 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- PCNT p.Ser1113Arg 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-ser1113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown