NM_000297.4(PKD2):c.570G>T (p.Ala190=) AND Polycystic kidney disease 2

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jul 23, 2021
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:: RCV001155350.5

Allele description [Variation Report for NM_000297.4(PKD2):c.570G>T (p.Ala190=)]

NM_000297.4(PKD2):c.570G>T (p.Ala190=)

Genes:

LOC129992813:ATAC-STARR-seq lymphoblastoid silent region 15559 [Gene]
PKD2:polycystin 2, transient receptor potential cation channel [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q22.1

Genomic location:

Preferred name:

NM_000297.4(PKD2):c.570G>T (p.Ala190=)

HGVS:

NC_000004.12:g.88008303G>T
NG_008604.1:g.5636G>T
NM_000297.4:c.570G>TMANE SELECT
NP_000288.1:p.Ala190=
NC_000004.11:g.88929455G>T
NM_000297.2:c.570G>T
NM_000297.3:c.570G>T
NR_156488.2:n.669G>T
p.Ala190Ala

Links:

dbSNP: rs541702320

NCBI 1000 Genomes Browser:

rs541702320

Molecular consequence:

NR_156488.2:n.669G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000297.4:c.570G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Polycystic kidney disease 2 (PKD2)
Synonyms:: POLYCYSTIC KIDNEY DISEASE, ADULT, TYPE II; POLYCYSTIC KIDNEY DISEASE 2 WITH OR WITHOUT POLYCYSTIC LIVER DISEASE
Identifiers:: MONDO: MONDO:0013131; MedGen: C2751306; OMIM: 613095

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hypothetical protein THICB310048 [Thiomonas sp. CB3]
hypothetical protein THICB310048 [Thiomonas sp. CB3]
gi|1026941775|emb|CQR41299.1||gnl|W RM|CQR41299

Protein
putative tonB protein [Thiomonas sp. CB3]
putative tonB protein [Thiomonas sp. CB3]
gi|1026941776|emb|CQR41300.1||gnl|W RM|CQR41300

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001316774	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 28, 2017)	germline	clinical testing	Citation Link,
SCV002805022	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 23, 2021)	unknown	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

SCV001316774

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 28, 2017)

germline

clinical testing

Citation Link,

SCV002805022

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 23, 2021)

unknown

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Illumina Laboratory Services, Illumina, SCV001316774.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

#	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 Fulgent Genetics, Fulgent Genetics, SCV002805022.1

#	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

Last Updated: Sep 29, 2024

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