Is TJP2 p.Pro484fs (c.1451del) pathogenic?

TJP2 p.Pro484fs (c.1451del) is classified Pathogenic in TJP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-05-02). No allele count reported in gnomAD v4.1 (AN 1,608,716).

How common is TJP2 p.Pro484fs (c.1451del) in the general population?

TJP2 p.Pro484fs (c.1451del) is no allele count reported in gnomAD v4.1 (AN 1,608,716) (gnomAD).

TJP2 p.Pro484fs

c.1451del · rs1554662952 · VCV501704

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,608,716)

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 9 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,608,716). 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: TJP2
Protein: p.Pro484fs
Coding: c.1451del
MANE Select: NM_004817
dbSNP: rs1554662952
Type: Deletion
Location: chr9:69228107 (GRCh38)
Gene constraint: LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 62.92 · 2 PDB
Residue 484: the 'disordered' region

Full TJP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TJP2 p.Arg775_Leu776insTer Pathogenic/Likely pathogenic ★★ same type
TJP2 p.Tyr261fs Pathogenic ★★ same type
TJP2 p.Arg197_Ser200del Uncertain significance ★★ same type
TJP2 p.Ser432del Uncertain significance ★★ same type
TJP2 c.1672-27del Benign ★★ same type
TJP2 c.239+14del Benign/Likely benign ★★ same type
TJP2 c.1517_1520+8del Likely pathogenic ★ same type
TJP2 c.952+1_952+732del 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/tjp2-p-pro484fs (accessed [today's date]).

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