NM_000458.4(HNF1B):c.187del (p.His63fs) AND Renal cysts and diabetes syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 14, 2019
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:: RCV001251471.3

Allele description [Variation Report for NM_000458.4(HNF1B):c.187del (p.His63fs)]

NM_000458.4(HNF1B):c.187del (p.His63fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_000458.4(HNF1B):c.187del (p.His63fs)

HGVS:

NC_000017.11:g.37744699del
NG_013019.2:g.5409del
NM_000458.4:c.187delMANE SELECT
NM_001165923.4:c.187del
NM_001304286.2:c.187del
NP_000449.1:p.His63fs
NP_001159395.1:p.His63fs
NP_001291215.1:p.His63fs
NC_000017.10:g.36104690del

Protein change:

H63fs

Links:

dbSNP: rs2034117925

NCBI 1000 Genomes Browser:

rs2034117925

Molecular consequence:

NM_000458.4:c.187del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001165923.4:c.187del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304286.2:c.187del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Renal cysts and diabetes syndrome (RCAD)
Synonyms:: Maturity-onset diabetes of the young, type 5; MODY type 5; Hyperuricemic nephropathy, familial juvenile, atypical; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007669; MedGen: C0431693; Orphanet: 93111; OMIM: 137920

Recent activity

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Taningia danae bio-material MNCN:DNA:239 cytochrome oxidase subunit I gene, part...
Taningia danae bio-material MNCN:DNA:239 cytochrome oxidase subunit I gene, partial cds; mitochondrial
gi|40068187|gb|AY393902.1|

Nucleotide
odLycHypo
odLycHypo
Lycopodina hypogea (LMA microbiome)

BioProject
pimr175 Pim proto-oncogene, serine/threonine kinase, related 175 [Danio rerio]
pimr175 Pim proto-oncogene, serine/threonine kinase, related 175 [Danio rerio]
Gene ID:568708

Gene
cand1 cullin-associated and neddylation-dissociated 1 [Danio rerio]
cand1 cullin-associated and neddylation-dissociated 1 [Danio rerio]
Gene ID:406806

Gene
ube2d2 ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast) [Danio rerio]
ube2d2 ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast) [Danio rerio]
Gene ID:393934

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001427192	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 14, 2019)	unknown	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

SCV001427192

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 14, 2019)

unknown

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	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001427192.2

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

Description

A heterozygous frameshift deletion variant, NM_000458.4(HNF1B):c.187del, has been identified in exon 1 of 9 of the HNF1B gene. This deletion is predicted to create a frameshift starting at amino acid position 63, introducing a stop codon 62 residues downstream (NP_000449.1(HNF1B):p.(His63Ilefs*62)). This variant is predicted to result in loss of protein function either through truncation (including HNF-1_N and downstream HNF-1B_C functional domains) or nonsense-mediated decay, which is a reported mechanism of pathogenicity for this gene. The variant is absent in population databases (gnomAD). This variant has not been previously reported in clinical cases. However, many other protein truncating variants in HNF1B have previously been reported as pathogenic in clinical cases (ClinVar, Decipher, HGMD, Alvelos, M. et al. (2015)). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC.

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

Last Updated: Jul 29, 2023

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Relating variation to medicine