NM_001009944.3(PKD1):c.10529C>T (p.Thr3510Met) AND Polycystic kidney disease, adult type

Germline classification:: Benign (2 submissions)
Last evaluated:: Feb 3, 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:: RCV000677315.12

Allele description [Variation Report for NM_001009944.3(PKD1):c.10529C>T (p.Thr3510Met)]

NM_001009944.3(PKD1):c.10529C>T (p.Thr3510Met)

Genes:

PKD1-AS1:PKD1 antisense RNA 1 [Gene - HGNC]
PKD1:polycystin 1, transient receptor potential channel interacting [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_001009944.3(PKD1):c.10529C>T (p.Thr3510Met)

Other names:

NM_000296.3(PKD1):c.10526C>T(p.Thr3509Met); NM_001009944.2(PKD1):c.10529C>T(p.Thr3510Met)

HGVS:

NC_000016.10:g.2094181G>A
NG_008617.1:g.49040C>T
NM_000296.4:c.10526C>T
NM_001009944.3:c.10529C>TMANE SELECT
NP_000287.4:p.Thr3509Met
NP_001009944.3:p.Thr3510Met
NC_000016.9:g.2144182G>A
NM_000296.3:c.10526C>T
NM_001009944.2:c.10529C>T
P98161:p.Thr3510Met

Protein change:

T3509M

Links:

UniProtKB: P98161#VAR_010091; dbSNP: rs45478794

NCBI 1000 Genomes Browser:

rs45478794

Molecular consequence:

NM_000296.4:c.10526C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001009944.3:c.10529C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Polycystic kidney disease, adult type (PKD1)
Synonyms:: Polycystic Kidney, Autosomal Dominant; POLYCYSTIC KIDNEY DISEASE, ADULT, TYPE I; Polycystic kidney disease 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008263; MedGen: C3149841; OMIM: 173900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000604704	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Feb 3, 2020)	germline	clinical testing	Citation Link,
SCV000803480	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 31, 2018)	unknown	curation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000604704

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Benign
(Feb 3, 2020)

germline

clinical testing

Citation Link,

SCV000803480

SIB Swiss Institute of Bioinformatics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(May 31, 2018)

unknown

curation

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	curation

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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000604704.4

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

From SIB Swiss Institute of Bioinformatics, SCV000803480.1

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

Description

This variant is interpreted as a Benign - Stand Alone, for Polycystic kidney disease 1, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: BA1 => Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.

#	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

ClinVar

Relating variation to medicine