PCNT p.Phe1940=
c.5820C>T · rs1379460400 · VCV2861727
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00225%, sas)
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 0.14 | GERP -1.4, phastCons 0.056 |
| Overall | ||
| CADD | 6.985 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00225%
South Asian · 2/88,988 alleles
Filtering AF
0.000373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00014%
Overall
0.000317%
5/1,578,892 alleles · very rare
exomes 3/1,426,670 · genomes 2/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00225% | 44,494 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,432 |
| African / African-American | 0.00134% | 74,460 |
| European (non-Finnish) | 8.54e-05% | 1,170,343 |
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.Phe1940=
- Coding
- c.5820C>T
- MANE Select
- NM_006031
- dbSNP
- rs1379460400
- Type
- single nucleotide variant
- Location
- chr21:46411893 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- PCNT p.Phe1940Ser Uncertain significance ★ ⚠ same residue
- PCNT p.Phe1940fs Pathogenic ★ 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
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-phe1940 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown