NM_001009944.3(PKD1):c.2534T>C (p.Leu845Ser) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Apr 18, 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:: RCV000712602.12

Allele description [Variation Report for NM_001009944.3(PKD1):c.2534T>C (p.Leu845Ser)]

NM_001009944.3(PKD1):c.2534T>C (p.Leu845Ser)

Gene:

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.2534T>C (p.Leu845Ser)

HGVS:

NC_000016.10:g.2114489A>G
NG_008617.1:g.26410T>C
NM_000296.4:c.2534T>C
NM_001009944.3:c.2534T>CMANE SELECT
NP_000287.4:p.Leu845Ser
NP_001009944.3:p.Leu845Ser
NC_000016.9:g.2164490A>G
NM_000296.3:c.2534T>C
NM_001009944.2:c.2534T>C
P98161:p.Leu845Ser
p.L845S

Protein change:

L845S; LEU845SER

Links:

UniProtKB: P98161#VAR_010086; OMIM: 601313.0012; dbSNP: rs199476100

NCBI 1000 Genomes Browser:

rs199476100

Molecular consequence:

NM_000296.4:c.2534T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001009944.3:c.2534T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Ribosomal protein L33 family protein [Arabidopsis thaliana]
Ribosomal protein L33 family protein [Arabidopsis thaliana]
gi|15230697|ref|NP_187283.1|

Protein

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
SCV000843119	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Nov 29, 2017)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 26632257, 10854095, 26139440, 10364515, 15772804, 22383692, 26467025
SCV000928064	Blueprint Genetics	criteria provided, single submitter (Blueprint Genetics Variant Classification Scheme)	Pathogenic (Nov 20, 2018)	germline	clinical testing	Citation Link,
SCV001982055	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Apr 18, 2024)	germline	clinical testing	Citation Link,
SCV005197162	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 27, 2022)	germline	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	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

Identification of novel PKD1 and PKD2 mutations in a Chinese population with autosomal dominant polycystic kidney disease.

Liu B, Chen SC, Yang YM, Yan K, Qian YQ, Zhang JY, Hu YT, Dong MY, Jin F, Huang HF, Xu CM.

Sci Rep. 2015 Dec 3;5:17468. doi: 10.1038/srep17468. Erratum in: Sci Rep. 2016 Feb 23;6:21578. doi: 10.1038/srep21578.

PubMed [citation]

PMID:: 26632257
PMCID:: PMC4668380

Novel mutations in the duplicated region of PKD1 gene.

Perrichot R, Mercier B, Quere I, Carre A, Simon P, Whebe B, Cledes J, Ferec C.

Eur J Hum Genet. 2000 May;8(5):353-9.

PubMed [citation]

PMID:: 10854095

See all PubMed Citations (8)

Details of each submission

From Athena Diagnostics, SCV000843119.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

#	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 Blueprint Genetics, SCV000928064.1

#	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 GeneDx, SCV001982055.6

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

Description

In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 10854095, 22508176, 10364515, 25266109, 15772804, 23300259, 22383692, 26632257, 31740684, 30816285, 33454723, 36186434, 35783601, 33532864, 37909612, Durkie2023[paper], 38224954, 38541974, 26139440)

#	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 Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005197162.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

ClinVar

Relating variation to medicine