NM_138694.4(PKHD1):c.75T>C (p.Ile25=) AND Autosomal recessive polycystic kidney disease

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Nov 17, 2023
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:: RCV001406905.9

Allele description [Variation Report for NM_138694.4(PKHD1):c.75T>C (p.Ile25=)]

NM_138694.4(PKHD1):c.75T>C (p.Ile25=)

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.75T>C (p.Ile25=)

HGVS:

NC_000006.12:g.52083233A>G
NG_008753.1:g.9393T>C
NM_138694.4:c.75T>CMANE SELECT
NM_170724.3:c.75T>C
NP_619639.3:p.Ile25=
NP_733842.2:p.Ile25=
NC_000006.11:g.51948031A>G

Links:

dbSNP: rs138600204

NCBI 1000 Genomes Browser:

rs138600204

Molecular consequence:

NM_138694.4:c.75T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_170724.3:c.75T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Autosomal recessive polycystic kidney disease (ARPKD)
Synonyms:: POLYCYSTIC KIDNEY AND HEPATIC DISEASE 1; POLYCYSTIC KIDNEY DISEASE, INFANTILE, TYPE I; Polycystic kidney disease, infantile type; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009889; MeSH: D017044; MedGen: C0085548; Orphanet: 731; Orphanet: 8378

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ART1 [Trachemys scripta elegans]
ART1 [Trachemys scripta elegans]
Gene ID:117871357

Gene
Chondroitin Lyases
Chondroitin Lyases
Enzymes which catalyze the elimination of delta-4,5-D-glucuronate residues from polysaccharides containing 1,4-beta-hexosaminyl and 1,3-beta-D-glucuronosyl or 1,3-alpha-L-idur...<br/>Year introduced: 1991(1976)

MeSH
Chondro-4-Sulfatase
Chondro-4-Sulfatase
An enzyme from the sulfuric ester hydrolase class that breaks down one of the products of the chondroitin lyase II reaction. EC 3.1.6.9.<br/>Year introduced: 1991(1976)

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001608867	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Nov 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002083427	Natera, Inc.	no assertion criteria provided	Likely benign (Aug 21, 2018)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001608867

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Nov 17, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002083427

Natera, Inc.

no assertion criteria provided

Likely benign
(Aug 21, 2018)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001608867.4

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002083427.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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