NM_138694.4(PKHD1):c.10859G>A (p.Arg3620His) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 26, 2022
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV003151109.2

Allele description [Variation Report for NM_138694.4(PKHD1):c.10859G>A (p.Arg3620His)]

NM_138694.4(PKHD1):c.10859G>A (p.Arg3620His)

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.10859G>A (p.Arg3620His)

HGVS:

NC_000006.12:g.51659267C>T
NG_008753.1:g.433359G>A
NM_138694.4:c.10859G>AMANE SELECT
NP_619639.3:p.Arg3620His
NC_000006.11:g.51524065C>T
NM_138694.3:c.10859G>A

Protein change:

R3620H

Links:

dbSNP: rs149163661

NCBI 1000 Genomes Browser:

rs149163661

Molecular consequence:

NM_138694.4:c.10859G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003839876	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Uncertain significance (Aug 26, 2022)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003839876

Genetic Services Laboratory, University of Chicago

no assertion criteria provided

Uncertain significance
(Aug 26, 2022)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV003839876.1

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

Description

DNA sequence analysis of the PKHD1 gene demonstrated a sequence change, c.10859G>A, in exon 61 that results in an amino acid change, p.Arg3620His. This sequence change has been described in the gnomAD database with a frequency of 0.16% in the African/African American subpopulation (dbSNP rs149163661). The p.Arg3620His change affects a moderately conserved amino acid residue located in a domain of the PKHD1 protein that is not known to be functional. The p.Arg3620His substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This sequence change does not appear to have been previously described in individuals with PKHD1-related disorders. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Arg3620His change remains unknown at this time.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 19, 2024

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