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NM_138694.4(PKHD1):c.3368G>A (p.Gly1123Asp) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 20, 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:
RCV001582373.1

Allele description [Variation Report for NM_138694.4(PKHD1):c.3368G>A (p.Gly1123Asp)]

NM_138694.4(PKHD1):c.3368G>A (p.Gly1123Asp)

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.3368G>A (p.Gly1123Asp)
HGVS:
  • NC_000006.12:g.52028348C>T
  • NG_008753.1:g.64278G>A
  • NM_138694.3:c.3368G>A
  • NM_138694.4:c.3368G>AMANE SELECT
  • NM_170724.3:c.3368G>A
  • NP_619639.3:p.Gly1123Asp
  • NP_733842.2:p.Gly1123Asp
  • NC_000006.11:g.51893146C>T
  • NM_138694.4:c.3368G>A
Protein change:
G1123D
Links:
dbSNP: rs148356158
NCBI 1000 Genomes Browser:
rs148356158
Molecular consequence:
  • NM_138694.4:c.3368G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_170724.3:c.3368G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001821333Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Aug 20, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001821333.1

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

Description

Variant summary: PKHD1 c.3368G>A (p.Gly1123Asp) results in a non-conservative amino acid change located in the IPT domain (IPR002909) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 3.6e-05 in 251350 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.3368G>A in individuals affected with Polycystic Kidney And Hepatic Disease and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Oct 13, 2024