NM_000297.4(PKD2):c.570G>T (p.Ala190=) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Nov 20, 2020
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:: RCV000712684.14

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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rplE [Clostridium botulinum A str. ATCC 3502]
rplE [Clostridium botulinum A str. ATCC 3502]
Gene ID:5187726

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000843203	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Dec 29, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000884377	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Sep 14, 2017)	germline	clinical testing	Citation Link,
SCV001829257	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Nov 20, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000843203

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Dec 29, 2017)

germline

clinical testing

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

SCV000884377

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(Sep 14, 2017)

germline

clinical testing

Citation Link,

SCV001829257

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Nov 20, 2020)

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

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

Details of each submission

From Athena Diagnostics, SCV000843203.1

#	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	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, SCV000884377.1

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

Description

The PKD2 c.570G>T; p.Ala190Ala variant (rs541702320) has not been reported in the medical literature, but is listed as likely neutral in the Mayo ADPKD database (see link). It is reported in ClinVar (Variation ID: 255795) and observed in the African population at an overall frequency of 2% (232/11682 alleles) in the Genome Aggregation Database. This is a synonymous variant in a nucleotide that is weakly conserved, and computational algorithms (Alamut v.2.11) predict no impact on splicing. Based on available information, this variant is considered likely 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 GeneDx, SCV001829257.1

#	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: May 7, 2024

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