Is TJP2 p.Pro660= (c.1980C>T) pathogenic?

TJP2 p.Pro660= (c.1980C>T) is classified Likely benign in TJP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-09-06). Very rare (popmax 0.0022%, sas); Associated with TJP2-related disorder.

What condition is associated with TJP2 p.Pro660= (c.1980C>T)?

TJP2 p.Pro660= (c.1980C>T) is associated with TJP2-related disorder (ClinVar).

How common is TJP2 p.Pro660= (c.1980C>T) in the general population?

TJP2 p.Pro660= (c.1980C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

TJP2 p.Pro660=

c.1980C>T · VCV3353460

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Conditions

TJP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.23	GERP -4.3, phastCons 0.98
Overall
CADD	7.384	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,080 alleles

Filtering AF 0.000688% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000539%

Overall 0.00105% 17/1,613,904 alleles · very rare exomes 12/1,461,734 · genomes 5/152,170 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,540
African / African-American	0.00133%	74,920
European (non-Finnish)	0.00119%	84,289

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: TJP2
Protein: p.Pro660=
Coding: c.1980C>T
MANE Select: NM_004817
Type: single nucleotide variant
Location: chr9:69236227 (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 660: the sh3 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-pro660 (accessed [today's date]).

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