NM_001386140.1(MTTP):c.2666C>A (p.Thr889Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 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:: RCV001345532.3

Allele description [Variation Report for NM_001386140.1(MTTP):c.2666C>A (p.Thr889Asn)]

NM_001386140.1(MTTP):c.2666C>A (p.Thr889Asn)

Gene:

MTTP:microsomal triglyceride transfer protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q23

Genomic location:

Preferred name:

NM_001386140.1(MTTP):c.2666C>A (p.Thr889Asn)

HGVS:

NC_000004.12:g.99622829C>A
NG_011469.1:g.63747C>A
NM_000253.4:c.2666C>A
NM_001300785.2:c.2417C>A
NM_001386140.1:c.2666C>AMANE SELECT
NP_000244.2:p.Thr889Asn
NP_001287714.2:p.Thr806Asn
NP_001373069.1:p.Thr889Asn
NC_000004.11:g.100543986C>A

Protein change:

T806N

Links:

dbSNP: rs1459889971

NCBI 1000 Genomes Browser:

rs1459889971

Molecular consequence:

NM_000253.4:c.2666C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001300785.2:c.2417C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386140.1:c.2666C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Halomonas maura strain CECT 5298 platanus_K_25_97_37, whole genome shotgun seque...
Halomonas maura strain CECT 5298 platanus_K_25_97_37, whole genome shotgun sequence
gi|2532898900|ref|NZ_JAUFPQ01000003 gnl|WGS:NZ_JAUFPQ01|platanus_K_25_97_37

Nucleotide
Halomonas maura strain CECT 5298 platanus_K_25_97_28, whole genome shotgun seque...
Halomonas maura strain CECT 5298 platanus_K_25_97_28, whole genome shotgun sequence
gi|2532898854|ref|NZ_JAUFPQ01000002 gnl|WGS:NZ_JAUFPQ01|platanus_K_25_97_28

Nucleotide
TRIM52 tripartite motif containing 52 [Homo sapiens]
TRIM52 tripartite motif containing 52 [Homo sapiens]
Gene ID:84851

Gene
TRPM4 transient receptor potential cation channel subfamily M member 4 [Homo sap...
TRPM4 transient receptor potential cation channel subfamily M member 4 [Homo sapiens]
Gene ID:54795

Gene
mogroside IE synthase isoform X2 [Arachis duranensis]
mogroside IE synthase isoform X2 [Arachis duranensis]
gi|2338599762|ref|XP_052116267.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001539655	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	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

SCV001539655

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001539655.2

#	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 threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 889 of the MTTP protein (p.Thr889Asn). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with MTTP-related conditions. ClinVar contains an entry for this variant (Variation ID: 989818). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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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