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NM_138694.4(PKHD1):c.10219C>T (p.Gln3407Ter) AND not provided

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Jun 7, 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:
RCV000627228.10

Allele description [Variation Report for NM_138694.4(PKHD1):c.10219C>T (p.Gln3407Ter)]

NM_138694.4(PKHD1):c.10219C>T (p.Gln3407Ter)

Gene:
PKHD1:PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p12.3
Genomic location:
Preferred name:
NM_138694.4(PKHD1):c.10219C>T (p.Gln3407Ter)
Other names:
p.Gln3407*
HGVS:
  • NC_000006.12:g.51659907G>A
  • NG_008753.1:g.432719C>T
  • NM_138694.4:c.10219C>TMANE SELECT
  • NP_619639.3:p.Gln3407Ter
  • NC_000006.11:g.51524705G>A
  • NM_138694.3:c.10219C>T
Protein change:
Q3407*
Links:
dbSNP: rs781368899
NCBI 1000 Genomes Browser:
rs781368899
Molecular consequence:
  • NM_138694.4:c.10219C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
3

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000231864Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Pathogenic
(May 23, 2014)
germlineclinical testing

Citation Link,

SCV000748217GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Apr 17, 2023)
germlineclinical testing

Citation Link,

SCV001932182Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001954670Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV004226785Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 7, 2023)
germlineclinical testing

PubMed (11)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown3not providednot providednot providednot providedclinical testing

Citations

PubMed

PKHD1 mutations in autosomal recessive polycystic kidney disease (ARPKD).

Bergmann C, Senderek J, Küpper F, Schneider F, Dornia C, Windelen E, Eggermann T, Rudnik-Schöneborn S, Kirfel J, Furu L, Onuchic LF, Rossetti S, Harris PC, Somlo S, Guay-Woodford L, Germino GG, Moser M, Büttner R, Zerres K.

Hum Mutat. 2004 May;23(5):453-63. Review.

PubMed [citation]
PMID:
15108277

PKHD1 mutations in families requesting prenatal diagnosis for autosomal recessive polycystic kidney disease (ARPKD).

Bergmann C, Senderek J, Schneider F, Dornia C, Küpper F, Eggermann T, Rudnik-Schöneborn S, Kirfel J, Moser M, Büttner R, Zerres K.

Hum Mutat. 2004 May;23(5):487-95.

PubMed [citation]
PMID:
15108281
See all PubMed Citations (11)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000231864.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000748217.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28375157, 25525159, 15108281, 19176689, 16133180, 31589614, 32939031, 20460933)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001932182.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001954670.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV004226785.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (11)

Description

PM2_supporting, PM3, PS4_moderate, PVS1

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

Last Updated: Jul 23, 2024