NM_000527.5(LDLR):c.2083A>G (p.Thr695Ala) AND Familial hypercholesterolemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2021
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:: RCV001228745.6

Allele description [Variation Report for NM_000527.5(LDLR):c.2083A>G (p.Thr695Ala)]

NM_000527.5(LDLR):c.2083A>G (p.Thr695Ala)

Gene:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.2083A>G (p.Thr695Ala)

HGVS:

NC_000019.10:g.11120465A>G
NG_009060.1:g.36085A>G
NM_000527.5:c.2083A>GMANE SELECT
NM_001195798.2:c.2083A>G
NM_001195799.2:c.1960A>G
NM_001195800.2:c.1579A>G
NM_001195803.2:c.1606+232A>G
NP_000518.1:p.Thr695Ala
NP_001182727.1:p.Thr695Ala
NP_001182728.1:p.Thr654Ala
NP_001182729.1:p.Thr527Ala
LRG_274t1:c.2083A>G
LRG_274:g.36085A>G
NC_000019.9:g.11231141A>G
NM_000527.4:c.2083A>G

Protein change:

T527A

Links:

dbSNP: rs1600744007

NCBI 1000 Genomes Browser:

rs1600744007

Molecular consequence:

NM_001195803.2:c.1606+232A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000527.5:c.2083A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.2083A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.1960A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1579A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial hypercholesterolemia
Identifiers:: MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

Recent activity

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phage portal protein [Streptococcus salivarius]
phage portal protein [Streptococcus salivarius]
gi|2567033109|ref|WP_306452956.1|

Protein
serine dehydratase beta chain, partial [Salmonella enterica]
serine dehydratase beta chain, partial [Salmonella enterica]
gi|565624627|ref|WP_023891915.1|

Protein
ABC transporter ATP-binding protein [Thomasclavelia spiroformis]
ABC transporter ATP-binding protein [Thomasclavelia spiroformis]
gi|490746648|ref|WP_004608956.1|

Protein
PREDICTED: Homo sapiens multiple inositol-polyphosphate phosphatase 1 (MINPP1), ...
PREDICTED: Homo sapiens multiple inositol-polyphosphate phosphatase 1 (MINPP1), transcript variant X1, mRNA
gi|2462522002|ref|XM_054367221.1|

Nucleotide
Pathogen: clinical or host-associated sample from Streptococcus agalactiae
Pathogen: clinical or host-associated sample from Streptococcus agalactiae

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001401161	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2021)	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

SCV001401161

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2021)

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, SCV001401161.4

#	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 with alanine at codon 695 of the LDLR protein (p.Thr695Ala). The threonine residue is highly conserved and there is a small physicochemical difference between threonine and alanine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with LDLR-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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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