NM_000545.8(HNF1A):c.947del (p.Lys316fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 27, 2022
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:: RCV002829504.2

Allele description

NM_000545.8(HNF1A):c.947del (p.Lys316fs)

Gene:

HNF1A:HNF1 homeobox A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q24.31

Genomic location:

Preferred name:

NM_000545.8(HNF1A):c.947del (p.Lys316fs)

HGVS:

NC_000012.12:g.120994397del
NG_011731.2:g.20652del
NM_000545.8:c.947delMANE SELECT
NM_001306179.2:c.947del
NM_001406915.1:c.947delA
NP_000536.5:p.Lys316Argfs
NP_000536.6:p.Lys316fs
NP_001293108.2:p.Lys316fs
NP_001393844.1:p.Lys316Argfs
LRG_522t1:c.947del
LRG_522:g.20652del
LRG_522p1:p.Lys316Argfs
NC_000012.11:g.121432199del
NC_000012.11:g.121432200del
NM_000545.5:c.947delA

Protein change:

K316fs

Molecular consequence:

NM_000545.8:c.947del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001306179.2:c.947del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406915.1:c.947delA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens DEAH-box helicase 32 (putative) (DHX32), transcript vari...
PREDICTED: Homo sapiens DEAH-box helicase 32 (putative) (DHX32), transcript variant X1, mRNA
gi|2462520029|ref|XM_054366278.1|

Nucleotide
MAP/microtubule affinity-regulating kinase 3 isoform X26 [Homo sapiens]
MAP/microtubule affinity-regulating kinase 3 isoform X26 [Homo sapiens]
gi|2462540282|ref|XP_054232052.1|

Protein
Mus musculus glycoprotein hormone beta 5, mRNA (cDNA clone MGC:171089 IMAGE:8862...
Mus musculus glycoprotein hormone beta 5, mRNA (cDNA clone MGC:171089 IMAGE:8862484), complete cds
gi|187956774|gb|BC139462.1|

Nucleotide
Mus musculus src family associated phosphoprotein 2, mRNA (cDNA clone MGC:5700 I...
Mus musculus src family associated phosphoprotein 2, mRNA (cDNA clone MGC:5700 IMAGE:3599914), complete cds
gi|13277601|gb|BC003711.1|

Nucleotide
MAP/microtubule affinity-regulating kinase 3 isoform X2 [Homo sapiens]
MAP/microtubule affinity-regulating kinase 3 isoform X2 [Homo sapiens]
gi|2462540234|ref|XP_054232028.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003217520	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 27, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15928245, 18003757, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003217520

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 27, 2022)

germline

clinical testing

PubMed (3)
[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

Half of clinically defined maturity-onset diabetes of the young patients in Denmark do not have mutations in HNF4A, GCK, and TCF1.

Johansen A, Ek J, Mortensen HB, Pedersen O, Hansen T.

J Clin Endocrinol Metab. 2005 Aug;90(8):4607-14. Epub 2005 May 31.

PubMed [citation]

PMID:: 15928245

The type and the position of HNF1A mutation modulate age at diagnosis of diabetes in patients with maturity-onset diabetes of the young (MODY)-3.

Bellanné-Chantelot C, Carette C, Riveline JP, Valéro R, Gautier JF, Larger E, Reznik Y, Ducluzeau PH, Sola A, Hartemann-Heurtier A, Lecomte P, Chaillous L, Laloi-Michelin M, Wilhem JM, Cuny P, Duron F, Guerci B, Jeandidier N, Mosnier-Pudar H, Assayag M, Dubois-Laforgue D, Velho G, et al.

Diabetes. 2008 Feb;57(2):503-8. Epub 2007 Nov 14.

PubMed [citation]

PMID:: 18003757

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003217520.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with HNF1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys316Argfs*26) in the HNF1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HNF1A are known to be pathogenic (PMID: 15928245, 18003757).

#	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: Feb 20, 2024

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