PCNT p.Phe395=
c.1185T>C · rs764314231 · VCV340469
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0383%, amr)
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 1 | GERP -0.18, phastCons 1 |
| Overall | ||
| CADD | 9.176 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0383%
Admixed American · 23/60,024 alleles
Filtering AF
0.0261%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0222%
Overall
0.00582%
94/1,614,076 alleles · ultra-rare
exomes 73/1,461,754 · genomes 21/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0383% | 2,610 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| European (non-Finnish) | 0.00509% | 19,666 |
| African / African-American | 0.004% | 25,017 |
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.Phe395=
- Coding
- c.1185T>C
- MANE Select
- NM_006031
- dbSNP
- rs764314231
- Type
- single nucleotide variant
- Location
- chr21:46349164 (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-phe395 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown