Is PTPRO p.Pro318fs (c.948_951dup) pathogenic?

PTPRO p.Pro318fs (c.948951dup) is classified Uncertain significance in PTPRO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-09-16). No gnomAD frequency available for this variant.

How common is PTPRO p.Pro318fs (c.948_951dup) in the general population?

PTPRO p.Pro318fs (c.948_951dup) is no gnomAD frequency available for this variant (gnomAD).

PTPRO p.Pro318fs

c.948_951dup · rs1565668100 · VCV591052

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

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.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP 1.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: PTPRO
Protein: p.Pro318fs
Coding: c.948_951dup
MANE Select: NM_030667
dbSNP: rs1565668100
Type: Duplication
Location: chr12:15501904 (GRCh38)
Gene constraint: LOEUF 0.513 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 77.55 · 2 PDB

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

Similar variants

PTPRO p.Pro318Leu Uncertain significance ★ ⚠ same residue
PTPRO c.1586-145dup Benign ★ same type
PTPRO c.1586-152_1586-145dup Benign ★ same type
PTPRO c.2711+17dup Benign ★ same type
PTPRO c.2997+18dup Benign ★ same type
PTPRO c.3256-168dup 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/ptpro-p-pro318fs (accessed [today's date]).

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