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NM_138694.4(PKHD1):c.9719G>T (p.Arg3240Leu) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Aug 5, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000153706.15

Allele description [Variation Report for NM_138694.4(PKHD1):c.9719G>T (p.Arg3240Leu)]

NM_138694.4(PKHD1):c.9719G>T (p.Arg3240Leu)

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.9719G>T (p.Arg3240Leu)
HGVS:
  • NC_000006.12:g.51747897C>A
  • NG_008753.1:g.344729G>T
  • NM_138694.4:c.9719G>TMANE SELECT
  • NM_170724.3:c.9719G>T
  • NP_619639.3:p.Arg3240Leu
  • NP_619639.3:p.Arg3240Leu
  • NP_733842.2:p.Arg3240Leu
  • NC_000006.11:g.51612695C>A
  • NM_138694.3:c.9719G>T
Protein change:
R3240L
Links:
dbSNP: rs146649803
NCBI 1000 Genomes Browser:
rs146649803
Molecular consequence:
  • NM_138694.4:c.9719G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170724.3:c.9719G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000203264Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Uncertain significance
(Mar 11, 2014) 		germlineclinical testing

Citation Link,

SCV004034360GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Aug 5, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000203264.7

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

From GeneDx, SCV004034360.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 9511976, 38300123, 38839463, 15805161, 15698423, 24162162)

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

Last Updated: Nov 24, 2024