PCNT p.Ala853Phe
c.2556_2559delinsCTTT · rs2146858439 · VCV1415785
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -3 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 121 kb · p 0.027 · regional, not allelic |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PCNT
- Protein
- p.Ala853Phe
- Coding
- c.2556_2559delinsCTTT
- MANE Select
- NM_006031
- dbSNP
- rs2146858439
- Type
- Indel
- Location
- chr21:46363881 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
Similar variants
- PCNT p.Ala853fs Pathogenic ★ same residue
- PCNT p.Ala853Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- PCNT p.Ala853= Likely benign ★ same residue
- PCNT p.Arg1903Phe Uncertain significance ★★ same type
- PCNT p.Glu2520fs Likely pathogenic ★ same type
- PCNT p.Val719_Lys720delinsPheAsnThrIleTer Likely pathogenic ★ same type
- PCNT p.Pro2193Arg Uncertain significance ★ same type
- PCNT p.Asn1841Ser Likely benign ★ 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-ala853phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown