NM_138694.4(PKHD1):c.100G>A (p.Gly34Arg) AND Polycystic kidney disease 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 14, 2021
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:: RCV001730184.2

Allele description [Variation Report for NM_138694.4(PKHD1):c.100G>A (p.Gly34Arg)]

NM_138694.4(PKHD1):c.100G>A (p.Gly34Arg)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

6p12.2

Genomic location:

Preferred name:

NM_138694.4(PKHD1):c.100G>A (p.Gly34Arg)

HGVS:

NC_000006.12:g.52083208C>T
NG_008753.1:g.9418G>A
NM_138694.4:c.100G>AMANE SELECT
NM_170724.3:c.100G>A
NP_619639.3:p.Gly34Arg
NP_733842.2:p.Gly34Arg
NC_000006.11:g.51948006C>T
NM_138694.3:c.100G>A

Protein change:

G34R

Links:

dbSNP: rs2128244638

NCBI 1000 Genomes Browser:

rs2128244638

Molecular consequence:

NM_138694.4:c.100G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_170724.3:c.100G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001977608	Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 14, 2021)	paternal	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

SCV001977608

Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 14, 2021)

paternal

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	paternal	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 Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, SCV001977608.1

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

Description

The variant has not yet been listed in the dbSNP database or in gnomAD or ClinVar (as of October 12, 2021). It has already been reported in the literature as a "variant of uncertain significance" in a patient with the clinical diagnosis of ARPKD in compound heterozygosity with another PKHD1 variant classified as likely pathogenic (Obeidova et al., 2020). In bioinformatics, the change is classified as "disease causing" (CADDphred 32). Based on the current state of knowledge, the variant is to be classified as a "variant of unclear clinical significance" (ACMG criteria).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	paternal	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 30, 2024

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Relating variation to medicine