NM_138694.4(PKHD1):c.462T>C (p.His154=) AND Autosomal recessive polycystic kidney disease

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 25, 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:: RCV001393717.7

Allele description [Variation Report for NM_138694.4(PKHD1):c.462T>C (p.His154=)]

NM_138694.4(PKHD1):c.462T>C (p.His154=)

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.462T>C (p.His154=)

HGVS:

NC_000006.12:g.52073528A>G
NG_008753.1:g.19098T>C
NM_138694.4:c.462T>CMANE SELECT
NM_170724.3:c.462T>C
NP_619639.3:p.His154=
NP_733842.2:p.His154=
NC_000006.11:g.51938326A>G

Links:

dbSNP: rs779580027

NCBI 1000 Genomes Browser:

rs779580027

Molecular consequence:

NM_138694.4:c.462T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_170724.3:c.462T>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

Recent activity

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PREDICTED: Rattus norvegicus proline-rich coiled-coil 2A (Prrc2a), transcript va...
PREDICTED: Rattus norvegicus proline-rich coiled-coil 2A (Prrc2a), transcript variant X7, mRNA
gi|2678923812|ref|XM_006256053.5|

Nucleotide
Rattus norvegicus RNA helicase with arginine-serine-rich domain mRNA, complete c...
Rattus norvegicus RNA helicase with arginine-serine-rich domain mRNA, complete cds
gi|897914|gb|U25746.1|RNU25746

Nucleotide
RecName: Full=Protein PRRC2A; AltName: Full=HLA-B-associated transcript 2; AltNa...
RecName: Full=Protein PRRC2A; AltName: Full=HLA-B-associated transcript 2; AltName: Full=Proline-rich and coiled-coil-containing protein 2A
gi|73619525|sp|Q6MG48.1|PRC2A_RAT

Protein
Milieu Therapy
Milieu Therapy
A treatment program based on manipulation of the patient's environment by the medical staff. The patient does not participate in planning the treatment regimen....<br/>Year introduced: 1969(1967)

MeSH
NAD(P)-binding Rossmann-fold superfamily protein isoform 1 [Theobroma cacao]
NAD(P)-binding Rossmann-fold superfamily protein isoform 1 [Theobroma cacao]
gi|590698175|ref|XP_007045644.1||gn _WGS:ALXC|Thecc1EG011349p1

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001595391	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Apr 25, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001595391

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Apr 25, 2023)

germline

clinical testing

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

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, SCV001595391.4

#	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

Last Updated: Sep 29, 2024

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