NM_138694.4(PKHD1):c.449-15TTC[2] AND Autosomal recessive polycystic kidney disease

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 29, 2024
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:: RCV000233390.14

Allele description [Variation Report for NM_138694.4(PKHD1):c.449-15TTC[2]]

NM_138694.4(PKHD1):c.449-15TTC[2]

Gene:

PKHD1:PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

6p12.2

Genomic location:

Preferred name:

NM_138694.4(PKHD1):c.449-15TTC[2]

HGVS:

NC_000006.12:g.52073548GAA[2]
NG_008753.1:g.19070TTC[2]
NM_138694.4:c.449-15TTC[2]MANE SELECT
NM_170724.3:c.449-15TTC[2]
NC_000006.11:g.51938346GAA[2]
NC_000006.11:g.51938346_51938348del
NM_138694.3:c.449-9_449-7del
NM_138694.3:c.449-9_449-7delTTC
NM_138694.4:c.449-9_449-7delMANE SELECT
NM_170724.3:c.449-9_449-7del

Links:

dbSNP: rs545812620

NCBI 1000 Genomes Browser:

rs545812620

Molecular consequence:

NM_138694.4:c.449-15TTC[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_170724.3:c.449-15TTC[2] - intron variant - [Sequence Ontology: SO:0001627]

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

Recent activity

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PREDICTED: Rattus norvegicus regulator of G-protein signaling 6 (Rgs6), transcri...
PREDICTED: Rattus norvegicus regulator of G-protein signaling 6 (Rgs6), transcript variant X2, mRNA
gi|2678952964|ref|XM_039112783.2|

Nucleotide
protein angel homolog 2 isoform X1 [Rattus norvegicus]
protein angel homolog 2 isoform X1 [Rattus norvegicus]
gi|1958672639|ref|XP_038946748.1|

Protein
protein angel homolog 2 isoform X3 [Rattus norvegicus]
protein angel homolog 2 isoform X3 [Rattus norvegicus]
gi|1958672648|ref|XP_038946752.1|

Protein
PREDICTED: Rattus norvegicus angel homolog 2 (Angel2), transcript variant X5, mR...
PREDICTED: Rattus norvegicus angel homolog 2 (Angel2), transcript variant X5, mRNA
gi|2678891969|ref|XM_006250462.5|

Nucleotide
UDP-glucuronosyltransferase 2B2 precursor [Rattus norvegicus]
UDP-glucuronosyltransferase 2B2 precursor [Rattus norvegicus]
gi|1983576028|ref|NP_113721.5|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000291334	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002083406	Natera, Inc.	no assertion criteria provided	Benign (Nov 15, 2017)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000291334

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 29, 2024)

germline

clinical testing

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

SCV002083406

Natera, Inc.

no assertion criteria provided

Benign
(Nov 15, 2017)

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, SCV000291334.9

#	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., SCV002083406.1

#	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: Oct 13, 2024

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