NM_005529.7(HSPG2):c.12992G>A (p.Ser4331Asn) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV001511116.8

Allele description

NM_005529.7(HSPG2):c.12992G>A (p.Ser4331Asn)

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.12992G>A (p.Ser4331Asn)

HGVS:

NC_000001.11:g.21823627C>T
NG_016740.1:g.118631G>A
NM_001013693.3:c.*1412C>TMANE SELECT
NM_001291860.2:c.12995G>A
NM_005529.7:c.12992G>AMANE SELECT
NP_001278789.1:p.Ser4332Asn
NP_005520.4:p.Ser4331Asn
NC_000001.10:g.22150120C>T
NM_005529.5:c.12992G>A
P98160:p.Ser4331Asn

Protein change:

S4331N

Links:

UniProtKB: P98160#VAR_047995; dbSNP: rs3736360

NCBI 1000 Genomes Browser:

rs3736360

Molecular consequence:

NM_001013693.3:c.*1412C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001291860.2:c.12995G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005529.7:c.12992G>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
SCV001718305	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001859356	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Aug 19, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001718305

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 31, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001859356

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Aug 19, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 Invitae, SCV001718305.4

#	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 GeneDx, SCV001859356.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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