NM_001009944.3(PKD1):c.8791+1G>A AND Polycystic kidney disease, adult type

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 15, 2019
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:: RCV001267671.1

Allele description [Variation Report for NM_001009944.3(PKD1):c.8791+1G>A]

NM_001009944.3(PKD1):c.8791+1G>A

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.8791+1G>A

HGVS:

NC_000016.10:g.2103265C>T
NG_008617.1:g.39956G>A
NM_000296.4:c.8791+1G>A
NM_001009944.3:c.8791+1G>AMANE SELECT
NC_000016.9:g.2153266C>T
NM_001009944.2:c.8791+1G>A

Links:

dbSNP: rs2092177236

NCBI 1000 Genomes Browser:

rs2092177236

Molecular consequence:

NM_000296.4:c.8791+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001009944.3:c.8791+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001445904	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 15, 2019)	germline	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

SCV001445904

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 15, 2019)

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

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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV001445904.1

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

Description

This variant affects the canonical splice donor site of intron 23 of 45, and is therefore predicted to interfere with splicing and result in loss of normal protein function. This variant has been previously reported as a heterozygous change in patients with autosomal dominant polycystic kidney disease (PMID: 24611717). It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Multiple splice prediction tools suggest this variant is likely to interfere with normal splicing. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.8791+1G>A variant is classified as Pathogenic.

#	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: Aug 5, 2023

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