NM_005529.7(HSPG2):c.13018G>A (p.Val4340Met) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Jan 8, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000711913.33

Allele description [Variation Report for NM_005529.7(HSPG2):c.13018G>A (p.Val4340Met)]

NM_005529.7(HSPG2):c.13018G>A (p.Val4340Met)

Genes:

HSPG2:heparan sulfate proteoglycan 2 [Gene - OMIM - HGNC]
LDLRAD2:low density lipoprotein receptor class A domain containing 2 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.12

Genomic location:

Preferred name:

NM_005529.7(HSPG2):c.13018G>A (p.Val4340Met)

HGVS:

NC_000001.11:g.21823474C>T
NG_016740.1:g.118784G>A
NM_001013693.3:c.*1259C>TMANE SELECT
NM_001291860.2:c.13021G>A
NM_005529.7:c.13018G>AMANE SELECT
NP_001278789.1:p.Val4341Met
NP_005520.4:p.Val4340Met
NC_000001.10:g.22149967C>T
NM_005529.5:c.13018G>A
NM_005529.6:c.13018G>A

Protein change:

V4340M

Links:

dbSNP: rs145687082

NCBI 1000 Genomes Browser:

rs145687082

Molecular consequence:

NM_001013693.3:c.*1259C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001291860.2:c.13021G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005529.7:c.13018G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000704931	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Jan 26, 2017)	germline	clinical testing	Citation Link,
SCV000842324	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Sep 30, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25504735, 26467025
SCV000884016	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Likely benign (Oct 26, 2023)	germline	clinical testing	Citation Link,
SCV001035166	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 8, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003809223	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 14, 2019)	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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Exome sequencing identifies a rare HSPG2 variant associated with familial idiopathic scoliosis.

Baschal EE, Wethey CI, Swindle K, Baschal RM, Gowan K, Tang NL, Alvarado DM, Haller GE, Dobbs MB, Taylor MR, Gurnett CA, Jones KL, Miller NH.

G3 (Bethesda). 2014 Dec 12;5(2):167-74. doi: 10.1534/g3.114.015669.

PubMed [citation]

PMID:: 25504735
PMCID:: PMC4321025

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

See all PubMed Citations (4)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000704931.2

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

#	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		1	not provided	not provided	not provided

From Athena Diagnostics, SCV000842324.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884016.4

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

#	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

From Invitae, SCV001035166.6

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

#	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

From Revvity Omics, Revvity, SCV003809223.2

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

#	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: Jul 29, 2024

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