ClinVar Genomic variation as it relates to human health
NM_138694.4(PKHD1):c.5221G>A (p.Val1741Met)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Pathogenic(1); Likely pathogenic(3); Uncertain significance(5)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_138694.4(PKHD1):c.5221G>A (p.Val1741Met)
Variation ID: 4111 Accession: VCV000004111.55
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6p12.2 6: 52024589 (GRCh38) [ NCBI UCSC ] 6: 51889387 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 29, 2015 Oct 8, 2024 Mar 28, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_138694.4:c.5221G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_619639.3:p.Val1741Met missense NM_170724.3:c.5221G>A NP_733842.2:p.Val1741Met missense NC_000006.12:g.52024589C>T NC_000006.11:g.51889387C>T NG_008753.1:g.68037G>A P08F94:p.Val1741Met - Protein change
- V1741M
- Other names
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- Canonical SPDI
- NC_000006.12:52024588:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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LOC126859690 | - | - | - | GRCh38 | - | 203 |
PKHD1 | - | - |
GRCh38 GRCh37 |
5041 | 5256 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Conflicting interpretations of pathogenicity (5) |
criteria provided, conflicting classifications
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Nov 20, 2023 | RCV000004327.20 | |
Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
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Mar 28, 2024 | RCV000153715.14 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Dec 27, 2023 | RCV001849254.12 | |
See cases
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Uncertain significance (1) |
criteria provided, single submitter
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Dec 21, 2021 | RCV004584313.1 |
PKHD1-related disorder
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Likely pathogenic (1) |
no assertion criteria provided
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May 6, 2024 | RCV004748495.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Mar 11, 2014)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000203273.7
First in ClinVar: Feb 02, 2015 Last updated: Jun 29, 2015 |
Number of individuals with the variant: 2
Sex: mixed
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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease 4
Affected status: unknown
Allele origin:
germline
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Baylor Genetics
Accession: SCV001163045.1
First in ClinVar: Feb 29, 2020 Last updated: Feb 29, 2020 |
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Pathogenic
(Nov 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive polycystic kidney disease
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV002231162.4
First in ClinVar: Mar 28, 2022 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 1741 of the PKHD1 protein (p.Val1741Met). … (more)
This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 1741 of the PKHD1 protein (p.Val1741Met). This variant is present in population databases (rs137852946, gnomAD 0.006%). This missense change has been observed in individual(s) with clinical features of polycystic kidney disease (PMID: 11919560, 12846734, 19914852, 30773290; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 4111). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PKHD1 protein function. For these reasons, this variant has been classified as Pathogenic. (less)
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Uncertain significance
(Dec 21, 2021)
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criteria provided, single submitter
Method: clinical testing
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see cases
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University Hospital Muenster
Accession: SCV002577855.2
First in ClinVar: Oct 08, 2022 Last updated: Jul 07, 2024 |
Comment:
ACMG categories: PM1,PM2,PP3
Number of individuals with the variant: 1
Clinical Features:
Kidney disorder (present)
Age: 0-9 years
Sex: male
Tissue: blood
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Uncertain significance
(Aug 02, 2017)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease 4
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000800567.1
First in ClinVar: Oct 11, 2015 Last updated: Oct 11, 2015 |
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Likely pathogenic
(Feb 05, 2020)
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criteria provided, single submitter
Method: research
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Polycystic kidney disease 4
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
unknown
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Cavalleri Lab, Royal College of Surgeons in Ireland
Accession: SCV001251234.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
PS1, PM3, PP2, PP3, PP4
Clinical Features:
Polycystic kidney dysplasia (present)
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Likely pathogenic
(Dec 27, 2023)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease 4
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004204535.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
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Uncertain significance
(Jul 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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Polycystic kidney disease 4
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV005086325.1
First in ClinVar: Jul 23, 2024 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0102 - Loss of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with polycystic kidney disease 4, with or without hepatic disease (MIM#263200). (I) 0106 - This gene is associated with autosomal recessive disease; however, there are emerging reports of heterozygous carriers of PKHD1 variants developing liver cysts and nephrocalcinosis (PMID: 21945273). (I) 0115 - Variants in this gene are known to have variable expressivity. Significant intrafamilial variability has been reported (PMID: 20301501). (I) 0200 - Variant is predicted to result in a missense amino acid change from valine to methionine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 (9 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been classified as pathogenic, likely pathogenic and as a VUS by clinical laboratories in ClinVar. This variant has also been observed in the literature as a single heterozygous variant, with other PKHD1 variants (not confirmed to be in trans), and also as homozygous in individuals with ARPKD or related phenotypes (PMIDs: 21945273, 11919560, 12846734, 19914852, 20413436, 30773290, 35372954). (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Uncertain significance
(Mar 28, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV004039701.2
First in ClinVar: Oct 07, 2023 Last updated: Sep 16, 2024 |
Comment:
Identified as a single heterozygous variant in an individual with polycystic kidney disease and in an individual with liver cysts (PMID: 11919560, 21945273); Not observed … (more)
Identified as a single heterozygous variant in an individual with polycystic kidney disease and in an individual with liver cysts (PMID: 11919560, 21945273); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 21945273, 30773290, 35372954, 12846734, 34405919, 11919560, 33454723) (less)
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Pathogenic
(Mar 01, 2002)
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no assertion criteria provided
Method: literature only
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POLYCYSTIC KIDNEY DISEASE 4
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000024498.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 11, 2015 |
Comment on evidence:
In a man in whom the diagnosis of autosomal recessive polycystic kidney disease (PKD4; 263200) was first made at the age of 25 years on … (more)
In a man in whom the diagnosis of autosomal recessive polycystic kidney disease (PKD4; 263200) was first made at the age of 25 years on the basis of flank pain, Ward et al. (2002) found a val1741-to-met (V1741M) missense mutation in exon 32 of the PKHD1 gene, resulting from a 5221G-A nucleotide change. He had polycystic kidneys by renal imaging, but predominant changes were in the liver, which showed both congenital hepatic fibrosis and Caroli disease. He had esophageal varices, cholangitis, and splenomegaly. The patient did not have hypertension, and serum creatinine at the age of 41 years was 1.8. (less)
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Pathogenic
(Feb 14, 2019)
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no assertion criteria provided
Method: literature only
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Polycystic kidney disease 4
Affected status: yes
Allele origin:
germline
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Yale Center for Mendelian Genomics, Yale University
Study: Yale Center for Mendelian Genomics
Accession: SCV002106588.1 First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022 |
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Likely pathogenic
(May 06, 2024)
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no assertion criteria provided
Method: clinical testing
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PKHD1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV005352429.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The PKHD1 c.5221G>A variant is predicted to result in the amino acid substitution p.Val1741Met. This variant has been reported in individuals with polycystic kidney disease … (more)
The PKHD1 c.5221G>A variant is predicted to result in the amino acid substitution p.Val1741Met. This variant has been reported in individuals with polycystic kidney disease (Ward et al. 2002. PubMed ID: 11919560; Connaughton et al. 2019. PubMed ID: 30773290; Table S3, Benson et al. 2021. PubMed ID: 33454723). This variant is reported in 0.0047% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as likely pathogenic. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Autosomal Recessive Polycystic Kidney Disease – PKHD1. | Adam MP | - | 2024 | PMID: 20301501 |
Beyond Panel-Based Testing: Exome Analysis Increases Sensitivity for Diagnosis of Genetic Kidney Disease. | Wilson PC | Kidney360 | 2020 | PMID: 35372954 |
Monogenic causes of chronic kidney disease in adults. | Connaughton DM | Kidney international | 2019 | PMID: 30773290 |
Hepatorenal findings in obligate heterozygotes for autosomal recessive polycystic kidney disease. | Gunay-Aygun M | Molecular genetics and metabolism | 2011 | PMID: 21945273 |
Correlation of kidney function, volume and imaging findings, and PKHD1 mutations in 73 patients with autosomal recessive polycystic kidney disease. | Gunay-Aygun M | Clinical journal of the American Society of Nephrology : CJASN | 2010 | PMID: 20413436 |
PKHD1 sequence variations in 78 children and adults with autosomal recessive polycystic kidney disease and congenital hepatic fibrosis. | Gunay-Aygun M | Molecular genetics and metabolism | 2010 | PMID: 19914852 |
Clinical and molecular characterization defines a broadened spectrum of autosomal recessive polycystic kidney disease (ARPKD). | Adeva M | Medicine | 2006 | PMID: 16523049 |
A complete mutation screen of PKHD1 in autosomal-recessive polycystic kidney disease (ARPKD) pedigrees. | Rossetti S | Kidney international | 2003 | PMID: 12846734 |
The gene mutated in autosomal recessive polycystic kidney disease encodes a large, receptor-like protein. | Ward CJ | Nature genetics | 2002 | PMID: 11919560 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PKHD1 | - | - | - | - |
Text-mined citations for rs137852946 ...
HelpRecord last updated Nov 03, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.