NM_138694.4(PKHD1):c.10233G>C (p.Val3411=) AND Autosomal recessive polycystic kidney disease

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 1, 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:: RCV001486110.7

Allele description [Variation Report for NM_138694.4(PKHD1):c.10233G>C (p.Val3411=)]

NM_138694.4(PKHD1):c.10233G>C (p.Val3411=)

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.10233G>C (p.Val3411=)

HGVS:

NC_000006.12:g.51659893C>G
NG_008753.1:g.432733G>C
NM_138694.4:c.10233G>CMANE SELECT
NP_619639.3:p.Val3411=
NC_000006.11:g.51524691C>G
NM_138694.3:c.10233G>C

Links:

dbSNP: rs1162292670

NCBI 1000 Genomes Browser:

rs1162292670

Molecular consequence:

NM_138694.4:c.10233G>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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Paracoccus sp. p1pa1 partial 16S rRNA gene, strain p1pa1
Paracoccus sp. p1pa1 partial 16S rRNA gene, strain p1pa1
gi|298286282|emb|FN811298.1|

Nucleotide
AL925245 PJR-Z1+Z2 Danio rerio cDNA clone 152-E05-2, mRNA sequence
AL925245 PJR-Z1+Z2 Danio rerio cDNA clone 152-E05-2, mRNA sequence
gi|23191825|gnl|dbEST|14038946|emb| 245.1|

Nucleotide
peroxisome biogenesis factor 2 [Homo sapiens]
peroxisome biogenesis factor 2 [Homo sapiens]
gi|1890266997|ref|NP_001165557.2|

Protein
RecName: Full=T-box transcription factor TBX4; Short=T-box protein 4
RecName: Full=T-box transcription factor TBX4; Short=T-box protein 4
gi|342187142|sp|P70325.3|TBX4_MOUSE

Protein
Methods - WHO Guidelines: Use of Cryotherapy for Cervical Intraepithelial Neopla...
Methods - WHO Guidelines: Use of Cryotherapy for Cervical Intraepithelial Neoplasia

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001690560	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jun 1, 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

SCV001690560

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jun 1, 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, SCV001690560.4

#	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: Oct 13, 2024

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