Is TJP2 p.Val712= (c.2136C>G) pathogenic?

TJP2 p.Val712= (c.2136C>G) is classified Likely benign in TJP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-04-27). Absent from gnomAD v4.1; Associated with TJP2-related disorder.

What condition is associated with TJP2 p.Val712= (c.2136C>G)?

TJP2 p.Val712= (c.2136C>G) is associated with TJP2-related disorder (ClinVar).

How common is TJP2 p.Val712= (c.2136C>G) in the general population?

TJP2 p.Val712= (c.2136C>G) is absent from gnomAD v4.1 (gnomAD).

TJP2 p.Val712=

c.2136C>G · rs2538581908 · VCV3051383

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

TJP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.26	donor gain · deltas
Constraint at this position
Conservation	phyloP -1.6	GERP -4.3
Overall
CADD	5.699	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TJP2
Protein: p.Val712=
Coding: c.2136C>G
MANE Select: NM_004817
dbSNP: rs2538581908
Type: single nucleotide variant
Location: chr9:69237093 (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 712: the guanylate kinase-like domain

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

Disease context

TJP2-related disorder

Similar variants

TJP2 c.61-7293C>G Uncertain significance ★★ same condition
TJP2 p.Arg951His Uncertain significance ★★ ⚠ same condition
TJP2 p.Arg970Gln Uncertain significance ★★ ⚠ same condition
TJP2 p.Thr1131Met Uncertain significance ★★ ⚠ same condition
TJP2 c.1319+2T>C Likely pathogenic ★ same condition
TJP2 p.Asp404Asn Conflicting classifications of pathogenicity ★ ⚠ same condition
TJP2 p.Glu401Gly Conflicting classifications of pathogenicity ★ ⚠ same condition
TJP2 p.Arg241Cys Uncertain significance ⚠ same condition

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-val712 (accessed [today's date]).

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