NM_001289104.2(PRKCSH):c.1378A>G (p.Ile460Val) AND not provided

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

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 1, 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:: RCV000966479.11

Allele description

NM_001289104.2(PRKCSH):c.1378A>G (p.Ile460Val)

Gene:

PRKCSH:PRKCSH beta subunit of glucosidase II [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_001289104.2(PRKCSH):c.1378A>G (p.Ile460Val)

HGVS:

NC_000019.10:g.11449092A>G
NG_009300.1:g.18639A>G
NM_001001329.3:c.1348A>G
NM_001289102.2:c.1348A>G
NM_001289103.2:c.1378A>G
NM_001289104.2:c.1378A>GMANE SELECT
NM_001379608.1:c.1357A>G
NM_001379609.1:c.1348A>G
NM_002743.3:c.1357A>G
NP_001001329.1:p.Ile450Val
NP_001276031.1:p.Ile450Val
NP_001276032.1:p.Ile460Val
NP_001276033.1:p.Ile460Val
NP_001366537.1:p.Ile453Val
NP_001366538.1:p.Ile450Val
NP_002734.2:p.Ile453Val
NC_000019.9:g.11559907A>G
NM_002743.2:c.1357A>G

Protein change:

I450V

Links:

dbSNP: rs34351170

NCBI 1000 Genomes Browser:

rs34351170

Molecular consequence:

NM_001001329.3:c.1348A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001289102.2:c.1348A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001289103.2:c.1378A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001289104.2:c.1378A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379608.1:c.1357A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001379609.1:c.1348A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002743.3:c.1357A>G - 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
SCV001113807	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 16, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001791733	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jan 11, 2021)	germline	clinical testing	Citation Link,
SCV005041402	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Apr 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001113807

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 16, 2024)

germline

clinical testing

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

SCV001791733

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Jan 11, 2021)

germline

clinical testing

Citation Link,

SCV005041402

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Apr 1, 2024)

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	1	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, SCV001113807.5

#	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, SCV001791733.1

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV005041402.2

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

Description

PRKCSH: BP4, BS1, BS2

#	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		1	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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