NM_001289104.2(PRKCSH):c.1290C>G (p.Tyr430Ter) AND Polycystic liver disease 1

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Aug 3, 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:: RCV000014147.30

Allele description [Variation Report for NM_001289104.2(PRKCSH):c.1290C>G (p.Tyr430Ter)]

NM_001289104.2(PRKCSH):c.1290C>G (p.Tyr430Ter)

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.1290C>G (p.Tyr430Ter)

Other names:

Y422*

HGVS:

NC_000019.10:g.11448917C>G
NG_009300.1:g.18464C>G
NM_001001329.3:c.1260C>G
NM_001289102.2:c.1260C>G
NM_001289103.2:c.1290C>G
NM_001289104.2:c.1290C>GMANE SELECT
NM_001379608.1:c.1269C>G
NM_001379609.1:c.1260C>G
NM_002743.3:c.1269C>G
NP_001001329.1:p.Tyr420Ter
NP_001276031.1:p.Tyr420Ter
NP_001276032.1:p.Tyr430Ter
NP_001276033.1:p.Tyr430Ter
NP_001366537.1:p.Tyr423Ter
NP_001366538.1:p.Tyr420Ter
NP_002734.2:p.Tyr423Ter
NC_000019.9:g.11559732C>G
NM_001289104.2:c.1290C>G

Protein change:

Y420*; TYR422TER

Links:

OMIM: 177060.0005; dbSNP: rs121918520

NCBI 1000 Genomes Browser:

rs121918520

Molecular consequence:

NM_001001329.3:c.1260C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001289102.2:c.1260C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001289103.2:c.1290C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001289104.2:c.1290C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001379608.1:c.1269C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001379609.1:c.1260C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_002743.3:c.1269C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Polycystic liver disease 1 (PCLD1)
Synonyms:: POLYCYSTIC LIVER DISEASE 1 WITH OR WITHOUT KIDNEY CYSTS
Identifiers:: MONDO: MONDO:0008265; MedGen: C0887850; Orphanet: 2924; OMIM: 174050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000034395	OMIM	no assertion criteria provided	Pathogenic (Mar 1, 2003)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002815259	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 3, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004024142	Genomics And Bioinformatics Analysis Resource, Columbia University	no assertion criteria provided	Pathogenic	unknown	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000034395

OMIM

no assertion criteria provided

Pathogenic
(Mar 1, 2003)

germline

literature only

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

SCV002815259

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 3, 2021)

unknown

clinical testing

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

SCV004024142

Genomics And Bioinformatics Analysis Resource, Columbia University

no assertion criteria provided

Pathogenic

unknown

research

Help

Summary from all submissions

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

Citations

PubMed

Mutations in PRKCSH cause isolated autosomal dominant polycystic liver disease.

Li A, Davila S, Furu L, Qian Q, Tian X, Kamath PS, King BF, Torres VE, Somlo S.

Am J Hum Genet. 2003 Mar;72(3):691-703. Epub 2003 Jan 15.

PubMed [citation]

PMID:: 12529853
PMCID:: PMC1180260

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV000034395.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a family in which 3 members had autosomal dominant polycystic liver disease-1 without kidney cysts (PCLD1; 174050), Li et al. (2003) found a 1266C-G transversion in exon 15 of the PRKCSH gene resulting in a nonsense mutation, tyr422 to stop (Y422X).

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

From Fulgent Genetics, Fulgent Genetics, SCV002815259.1

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

From Genomics And Bioinformatics Analysis Resource, Columbia University, SCV004024142.1

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

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

Last Updated: May 7, 2024

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