NM_138694.4(PKHD1):c.9559del (p.Ser3187fs) AND Polycystic kidney disease 4

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jul 11, 2023
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:: RCV003462297.3

Allele description [Variation Report for NM_138694.4(PKHD1):c.9559del (p.Ser3187fs)]

NM_138694.4(PKHD1):c.9559del (p.Ser3187fs)

Gene:

PKHD1:PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6p12.3

Genomic location:

Preferred name:

NM_138694.4(PKHD1):c.9559del (p.Ser3187fs)

HGVS:

NC_000006.12:g.51748060del
NG_008753.1:g.344569del
NM_138694.4:c.9559delMANE SELECT
NM_170724.3:c.9559del
NP_619639.3:p.Ser3187fs
NP_733842.2:p.Ser3187fs
NC_000006.11:g.51612858del
NC_000006.11:g.51612858delA
NM_138694.3:c.9559del
NM_138694.3:c.9559delT

Protein change:

S3187fs

Links:

dbSNP: rs797045101

NCBI 1000 Genomes Browser:

rs797045101

Molecular consequence:

NM_138694.4:c.9559del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_170724.3:c.9559del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Polycystic kidney disease 4 (PKD4)
Synonyms:: POLYCYSTIC KIDNEY DISEASE 4 WITH OR WITHOUT POLYCYSTIC LIVER DISEASE; PKD3
Identifiers:: MONDO: MONDO:0033004; MedGen: C4540575; OMIM: 263200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004204724	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 22, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004238585	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 11, 2023)	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

SCV004204724

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 22, 2023)

unknown

clinical testing

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

SCV004238585

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 11, 2023)

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	unknown	unknown	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

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 Baylor Genetics, SCV004204724.1

#	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

From Revvity Omics, Revvity, SCV004238585.1

#	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

Last Updated: Sep 29, 2024

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