NM_000384.3(APOB):c.5863G>A (p.Val1955Met) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 27, 2022
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:: RCV001800842.6

Allele description [Variation Report for NM_000384.3(APOB):c.5863G>A (p.Val1955Met)]

NM_000384.3(APOB):c.5863G>A (p.Val1955Met)

Gene:

APOB:apolipoprotein B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p24.1

Genomic location:

Preferred name:

NM_000384.3(APOB):c.5863G>A (p.Val1955Met)

HGVS:

NC_000002.12:g.21011005C>T
NG_011793.1:g.38069G>A
NM_000384.3:c.5863G>AMANE SELECT
NP_000375.3:p.Val1955Met
NC_000002.11:g.21233877C>T
NM_000384.2:c.5863G>A

Protein change:

V1955M

Links:

dbSNP: rs368970025

NCBI 1000 Genomes Browser:

rs368970025

Molecular consequence:

NM_000384.3:c.5863G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PDCD4 programmed cell death 4 [Homo sapiens]
PDCD4 programmed cell death 4 [Homo sapiens]
Gene ID:27250

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002046653	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Feb 17, 2021)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 31150472, 26467025
SCV002599757	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 27, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002046653

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Feb 17, 2021)

unknown

clinical testing

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

SCV002599757

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 27, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Multiple rare and common variants in APOB gene locus associated with oxidatively modified low-density lipoprotein levels.

Khlebus E, Kutsenko V, Meshkov A, Ershova A, Kiseleva A, Shevtsov A, Shcherbakova N, Zharikova A, Lankin V, Tikhaze A, Chazova I, Yarovaya E, Drapkina O, Boytsov S.

PLoS One. 2019;14(5):e0217620. doi: 10.1371/journal.pone.0217620.

PubMed [citation]

PMID:: 31150472
PMCID:: PMC6544350

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002046653.1

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

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

From GeneDx, SCV002599757.3

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

Description

Reported in one patient with low LDL levels in published literature (Khlebus et al., 2019); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31150472)

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

Last Updated: Oct 26, 2024

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