Is PCNT p.Pro2193Arg (c.6578_6579delinsGA) pathogenic?

PCNT p.Pro2193Arg (c.65786579delinsGA) is classified Uncertain significance in PCNT (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-22). No gnomAD frequency available for this variant.

How common is PCNT p.Pro2193Arg (c.6578_6579delinsGA) in the general population?

PCNT p.Pro2193Arg (c.6578_6579delinsGA) is no gnomAD frequency available for this variant (gnomAD).

PCNT p.Pro2193Arg

c.6578_6579delinsGA · rs2518829807 · VCV1934240

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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 1.1	GERP -2.9, phastCons 0.003
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.Pro2193Arg
Coding: c.6578_6579delinsGA
MANE Select: NM_006031
dbSNP: rs2518829807
Type: Indel
Location: chr21:46416496 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)
Residue 2193: the 'disordered' region

Full PCNT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PCNT p.Pro2193= Benign ★★ same residue
PCNT p.Pro2193Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
PCNT p.Ala853Phe Uncertain significance ★★ same type
PCNT p.Arg1903Phe Uncertain significance ★★ same type
PCNT p.Glu2520fs Likely pathogenic ★ same type
PCNT p.Val719_Lys720delinsPheAsnThrIleTer Likely pathogenic ★ same type
PCNT p.Asn1841Ser Likely benign ★ same type
PCNT p.Ser629Lys 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-pro2193arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown