NM_000458.4(HNF1B):c.477del (p.Pro159_Met160insTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 19, 2021
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:: RCV002513268.4

Allele description [Variation Report for NM_000458.4(HNF1B):c.477del (p.Pro159_Met160insTer)]

NM_000458.4(HNF1B):c.477del (p.Pro159_Met160insTer)

Gene:

HNF1B:HNF1 homeobox B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_000458.4(HNF1B):c.477del (p.Pro159_Met160insTer)

HGVS:

NC_000017.11:g.37739507del
NG_013019.2:g.10600del
NM_000458.4:c.477delMANE SELECT
NM_001165923.4:c.477del
NM_001304286.2:c.477del
NP_000449.1:p.Pro159_Met160insTer
NP_001159395.1:p.Pro159_Met160insTer
NP_001291215.1:p.Pro159_Met160insTer
NC_000017.10:g.36099498del
NM_000458.2:c.477delT
NM_000458.3:c.477del
NM_000458.3:c.477delT
p.Met160fsX1

Links:

Molecular consequence:

NM_000458.4:c.477del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165923.4:c.477del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304286.2:c.477del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003443072	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 19, 2021)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 11085914, 24429398, 9398836, 12148114, 15068978, 20378641, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003443072

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 19, 2021)

germline

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

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

Mutations in the hepatocyte nuclear factor-1beta gene are associated with familial hypoplastic glomerulocystic kidney disease.

Bingham C, Bulman MP, Ellard S, Allen LI, Lipkin GW, Hoff WG, Woolf AS, Rizzoni G, Novelli G, Nicholls AJ, Hattersley AT.

Am J Hum Genet. 2001 Jan;68(1):219-24. Epub 2000 Nov 20.

PubMed [citation]

PMID:: 11085914
PMCID:: PMC1234916

Mutations in 12 known dominant disease-causing genes clarify many congenital anomalies of the kidney and urinary tract.

Hwang DY, Dworschak GC, Kohl S, Saisawat P, Vivante A, Hilger AC, Reutter HM, Soliman NA, Bogdanovic R, Kehinde EO, Tasic V, Hildebrandt F.

Kidney Int. 2014 Jun;85(6):1429-33. doi: 10.1038/ki.2013.508. Epub 2014 Jan 15.

PubMed [citation]

PMID:: 24429398
PMCID:: PMC4040148

See all PubMed Citations (7)

Details of each submission

From Invitae, SCV003443072.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 36849). This variant is also known as P159fsdelT. This premature translational stop signal has been observed in individual(s) with clinical features of HNF1B-related conditions (PMID: 11085914, 24429398). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Met160*) in the HNF1B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HNF1B are known to be pathogenic (PMID: 9398836, 12148114, 15068978, 20378641).

#	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: Apr 15, 2024

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