NM_004817.4(TJP2):c.3067_3068delinsTT (p.Ala1023Phe) AND TJP2-related condition

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 18, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003905550.1

Allele description [Variation Report for NM_004817.4(TJP2):c.3067_3068delinsTT (p.Ala1023Phe)]

NM_004817.4(TJP2):c.3067_3068delinsTT (p.Ala1023Phe)

Gene:

TJP2:tight junction protein 2 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

9q21.11

Genomic location:

Preferred name:

NM_004817.4(TJP2):c.3067_3068delinsTT (p.Ala1023Phe)

HGVS:

NC_000009.12:g.69251110_69251111delinsTT
NG_016342.2:g.155204_155205delinsTT
NM_001170414.2:c.2812-1705_2812-1704delinsTT
NM_001170415.1:c.2968_2969delinsTT
NM_001170416.2:c.3160_3161delinsTT
NM_001369870.1:c.2992_2993delinsTT
NM_001369871.1:c.2998_2999delinsTT
NM_001369872.1:c.2956_2957delinsTT
NM_001369873.1:c.2743_2744delinsTT
NM_001369874.1:c.2893-1705_2893-1704delinsTT
NM_001369875.1:c.3079_3080delinsTT
NM_004817.3:c.3067_3068delinsTT
NM_004817.4:c.3067_3068delinsTTMANE SELECT
NM_201629.3:c.2881-1705_2881-1704delinsTT
NP_001163886.1:p.Ala990Phe
NP_001163887.1:p.Ala1054Phe
NP_001356799.1:p.Ala998Phe
NP_001356800.1:p.Ala1000Phe
NP_001356801.1:p.Ala986Phe
NP_001356802.1:p.Ala915Phe
NP_001356804.1:p.Ala1027Phe
NP_004808.2:p.Ala1023Phe
LRG_1201t1:c.3067_3068delinsTT
LRG_1201:g.155204_155205delinsTT
LRG_1201p1:p.Ala1023Phe
NC_000009.11:g.71866026_71866027delinsTT
NG_016342.1:g.134803_134804delinsTT

Protein change:

A1000F

Links:

dbSNP: rs1554668727

NCBI 1000 Genomes Browser:

rs1554668727

Molecular consequence:

NM_001170414.2:c.2812-1705_2812-1704delinsTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001369874.1:c.2893-1705_2893-1704delinsTT - intron variant - [Sequence Ontology: SO:0001627]
NM_201629.3:c.2881-1705_2881-1704delinsTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001170415.1:c.2968_2969delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001170416.2:c.3160_3161delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001369870.1:c.2992_2993delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001369871.1:c.2998_2999delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001369872.1:c.2956_2957delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001369873.1:c.2743_2744delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_001369875.1:c.3079_3080delinsTT - missense variant - [Sequence Ontology: SO:0001583]
NM_004817.4:c.3067_3068delinsTT - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: TJP2-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004721596	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004721596

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 18, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004721596.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The TJP2 c.3067_3068delinsTT variant is predicted to result in an in-frame deletion and insertion. This variant has been reported in an individual with benign recurrent intrahepatic cholestasis (Kornitzer and Alvarez et al. 2021. PubMed ID: 37205944). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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