NM_001032283.3(TMPO):c.565+1587G>A AND Loeys-Dietz syndrome 2

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 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:: RCV003627342.1

Allele description

NM_001032283.3(TMPO):c.565+1587G>A

Gene:

TMPO:thymopoietin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q23.1

Genomic location:

Preferred name:

NM_001032283.3(TMPO):c.565+1587G>A

HGVS:

NC_000012.12:g.98533425G>A
NG_021393.1:g.22853G>A
NM_001032283.3:c.565+1587G>AMANE SELECT
NM_001032284.3:c.565+1587G>A
NM_001307975.2:c.565+1587G>A
NM_003276.2:c.1168G>A
NP_003267.1:p.Val390Ile
LRG_443t2:c.1168G>A
LRG_443:g.22853G>A
LRG_443p2:p.Val390Ile
NC_000012.11:g.98927203G>A

Protein change:

V390I

Molecular consequence:

NM_001032283.3:c.565+1587G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001032284.3:c.565+1587G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001307975.2:c.565+1587G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_003276.2:c.1168G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Loeys-Dietz syndrome 2 (LDS2)
Synonyms:: Loeys-Dietz syndrome type 1B; MARFAN SYNDROME, TYPE II; Loeys-Dietz syndrome type 2B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012427; MedGen: C2674574; Orphanet: 558; OMIM: 610168

Recent activity

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PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript var...
PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript variant X3, mRNA
gi|2462630417|ref|XM_054327524.1|

Nucleotide
PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript var...
PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript variant X2, mRNA
gi|2217393513|ref|XM_011545556.2|

Nucleotide
PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript var...
PREDICTED: Homo sapiens ribosomal protein S6 kinase A3 (RPS6KA3), transcript variant X10, mRNA
gi|2217393523|ref|XM_017029717.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004533564	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 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

SCV004533564

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 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

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 Invitae, SCV004533564.1

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

Description

This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 390 of the TMPO protein (p.Val390Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TMPO-related conditions. 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) performed at Invitae indicates that this missense variant is not expected to disrupt TMPO protein function. 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: Feb 28, 2024

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