NM_004817.4(TJP2):c.215G>C (p.Gly72Ala) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000597068.8

Allele description [Variation Report for NM_004817.4(TJP2):c.215G>C (p.Gly72Ala)]

NM_004817.4(TJP2):c.215G>C (p.Gly72Ala)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

9q21.11

Genomic location:

Preferred name:

NM_004817.4(TJP2):c.215G>C (p.Gly72Ala)

HGVS:

NC_000009.12:g.69216439G>C
NG_016342.2:g.120533G>C
NM_001170414.2:c.146G>C
NM_001170415.1:c.227G>C
NM_001170416.2:c.308G>C
NM_001369870.1:c.146G>C
NM_001369871.1:c.146G>C
NM_001369872.1:c.215G>C
NM_001369873.1:c.215G>C
NM_001369874.1:c.227G>C
NM_001369875.1:c.227G>C
NM_004817.4:c.215G>CMANE SELECT
NM_201629.3:c.215G>C
NP_001163885.1:p.Gly49Ala
NP_001163886.1:p.Gly76Ala
NP_001163887.1:p.Gly103Ala
NP_001356799.1:p.Gly49Ala
NP_001356800.1:p.Gly49Ala
NP_001356801.1:p.Gly72Ala
NP_001356802.1:p.Gly72Ala
NP_001356803.1:p.Gly76Ala
NP_001356804.1:p.Gly76Ala
NP_004808.2:p.Gly72Ala
NP_963923.1:p.Gly72Ala
LRG_1201t1:c.215G>C
LRG_1201:g.120533G>C
LRG_1201p1:p.Gly72Ala
NC_000009.11:g.71831355G>C
NG_016342.1:g.100132G>C

Protein change:

G103A

Links:

dbSNP: rs747848974

NCBI 1000 Genomes Browser:

rs747848974

Molecular consequence:

NM_001170414.2:c.146G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001170415.1:c.227G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001170416.2:c.308G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369870.1:c.146G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369871.1:c.146G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369872.1:c.215G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369873.1:c.215G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369874.1:c.227G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001369875.1:c.227G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004817.4:c.215G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201629.3:c.215G>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000709666	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Jun 30, 2017)	germline	clinical testing	Citation Link,
SCV002215033	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 17, 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

SCV000709666

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Jun 30, 2017)

germline

clinical testing

Citation Link,

SCV002215033

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 17, 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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Eurofins Ntd Llc (ga), SCV000709666.2

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

#	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		1	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002215033.3

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TJP2 protein function. This sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 72 of the TJP2 protein (p.Gly72Ala). This variant is present in population databases (rs747848974, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with TJP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 502801). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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