NM_000545.8(HNF1A):c.1380_1406del (p.Gln460_Leu468del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 1, 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:: RCV003227959.3

Allele description [Variation Report for NM_000545.8(HNF1A):c.1380_1406del (p.Gln460_Leu468del)]

NM_000545.8(HNF1A):c.1380_1406del (p.Gln460_Leu468del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12q24.31

Genomic location:

Preferred name:

NM_000545.8(HNF1A):c.1380_1406del (p.Gln460_Leu468del)

HGVS:

NC_000012.12:g.120997544_120997570del
NG_011731.2:g.23799_23825del
NM_000545.6:c.1380_1406del
NM_000545.8:c.1380_1406delMANE SELECT
NM_001306179.2:c.1380_1406del
NP_000536.6:p.Gln460_Leu468del
NP_001293108.2:p.Gln460_Leu468del
LRG_522t1:c.1380_1406del
LRG_522:g.23799_23825del
NC_000012.11:g.121435342_121435368del
NC_000012.11:g.121435347_121435373del
NM_000545.5:c.1380_1406del
NM_000545.5:c.1380_1406del27

Links:

dbSNP: rs544842497

NCBI 1000 Genomes Browser:

rs544842497

Molecular consequence:

NM_000545.8:c.1380_1406del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001306179.2:c.1380_1406del - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

Name:: Diabetes mellitus type 1 (T1D)
Synonyms:: Type I diabetes mellitus
Identifiers:: MONDO: MONDO:0005147; MedGen: C0011854; OMIM: 222100; Human Phenotype Ontology: HP:0100651

Name:: Type 1 diabetes mellitus 20 (T1D20)
Synonyms:: Diabetes mellitus, insulin-dependent, 20
Identifiers:: MONDO: MONDO:0012919; MedGen: C2675866; OMIM: 612520

Name:: Maturity-onset diabetes of the young type 3
Synonyms:: Diabetes mellitus MODY type 3; MODY hepatocyte nuclear factor-1-alpha related; MODY type 3; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010894; MedGen: C1838100; Orphanet: 552; OMIM: 600496

Name:: Type 2 diabetes mellitus
Synonyms:: DIABETES MELLITUS, TYPE 2, PROTECTION AGAINST; Type II diabetes mellitus; Diabetes mellitus, noninsulin-dependent, late onset
Identifiers:: MONDO: MONDO:0005148; MeSH: D003924; MedGen: C0011860; OMIM: 125853; Human Phenotype Ontology: HP:0005978

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003925175	New York Genome Center	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Mar 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003925175

New York Genome Center

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Mar 1, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	1	not provided	clinical testing

Details of each submission

From New York Genome Center, SCV003925175.1

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

Description

The c.1380_1406del variant identified in the HNF1A gene results in an in-frame deletion of 9 amino acids (p.Gln460_Leu468del) in the transactivation domain of the HNF1A protein (PMID: 26853433) and is expected to preserve the integrity of the reading frame. This variant has not been reported in affected individuals in the literature. The variant has 0.0002299 allele frequency in the gnomAD (v3.1.2) database (35 out of 152244 heterozygous alleles, no homozygotes) and 0.00005597 allele frequency in the gnomAD (v2.1.1) database (14 out of 250142 heterozygous alleles, no homozygotes). This variant is reported as a variant of uncertain significance in the ClinVar database (Variation ID: 1026109). Based on the available evidence, the heterozygous c.1380_1406del (p.Gln460_Leu468del) variant identified in the HNF1A gene is reported as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine