NM_004958.4(MTOR):c.4555G>A (p.Ala1519Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 4, 2022
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:: RCV001220198.8

Allele description [Variation Report for NM_004958.4(MTOR):c.4555G>A (p.Ala1519Thr)]

NM_004958.4(MTOR):c.4555G>A (p.Ala1519Thr)

Gene:

MTOR:mechanistic target of rapamycin kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.22

Genomic location:

Preferred name:

NM_004958.4(MTOR):c.4555G>A (p.Ala1519Thr)

HGVS:

NC_000001.11:g.11150141C>T
NG_033239.1:g.117411G>A
NM_004958.4:c.4555G>AMANE SELECT
NP_004949.1:p.Ala1519Thr
LRG_734t1:c.4555G>A
LRG_734:g.117411G>A
NC_000001.10:g.11210198C>T
NM_004958.3:c.4555G>A

Protein change:

A1519T

Links:

dbSNP: rs1644090362

NCBI 1000 Genomes Browser:

rs1644090362

Molecular consequence:

NM_004958.4:c.4555G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001392174	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 4, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29051493, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001392174

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 4, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Variation in a range of mTOR-related genes associates with intracranial volume and intellectual disability.

Reijnders MRF, Kousi M, van Woerden GM, Klein M, Bralten J, Mancini GMS, van Essen T, Proietti-Onori M, Smeets EEJ, van Gastel M, Stegmann APA, Stevens SJC, Lelieveld SH, Gilissen C, Pfundt R, Tan PL, Kleefstra T, Franke B, Elgersma Y, Katsanis N, Brunner HG.

Nat Commun. 2017 Oct 20;8(1):1052. doi: 10.1038/s41467-017-00933-6.

PubMed [citation]

PMID:: 29051493
PMCID:: PMC5648772

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001392174.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1519 of the MTOR protein (p.Ala1519Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with macrocephaly and intellectual disability (PMID: 29051493). ClinVar contains an entry for this variant (Variation ID: 948857). 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 expected to disrupt MTOR 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: Sep 29, 2024

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