NM_000545.8(HNF1A):c.1539C>T (p.Thr513=) AND Maturity-onset diabetes of the young type 3

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 12, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000030485.14

Allele description [Variation Report for NM_000545.8(HNF1A):c.1539C>T (p.Thr513=)]

NM_000545.8(HNF1A):c.1539C>T (p.Thr513=)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.31

Genomic location:

Preferred name:

NM_000545.8(HNF1A):c.1539C>T (p.Thr513=)

HGVS:

NC_000012.12:g.120999305C>T
NG_011731.2:g.25560C>T
NM_000545.6:c.1539C>T
NM_000545.8:c.1539C>TMANE SELECT
NM_001306179.2:c.1539C>T
NP_000536.6:p.Thr513=
NP_001293108.2:p.Thr513=
LRG_522t1:c.1539C>T
LRG_522:g.25560C>T
NC_000012.11:g.121437108C>T
NM_000545.5:c.1539C>T

Links:

dbSNP: rs193922584

NCBI 1000 Genomes Browser:

rs193922584

Molecular consequence:

NM_000545.8:c.1539C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001306179.2:c.1539C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000053155	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	likely benign (Aug 18, 2011)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000376722	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 12, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000053155

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

likely benign
(Aug 18, 2011)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000376722

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Jan 12, 2018)

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	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Early-onset Type II diabetes mellitus in Italian families due to mutations in the genes encoding hepatic nuclear factor 1 alpha and glucokinase.

Gragnoli C, Cockburn BN, Chiaramonte F, Gorini A, Marietti G, Marozzi G, Signorini AM.

Diabetologia. 2001 Oct;44(10):1326-9.

PubMed [citation]

PMID:: 11692182

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000053155.2

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

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 1
2	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 2

Co-occurrences

#	Zygosity	Alleles	Number of Observations
1	SingleHeterozygote	TCF1:c.79A>C, TCF1:c.51C>G, TCF1:c.1460G>A, TCF1:c.1375C>T, TCF1:c.1501+7G>A, TCF1:c.1720A>G, TCF1:c.336G>A	1
2	SingleHeterozygote	TCF1:c.79A>C, TCF1:c.51C>G, TCF1:c.1501+7G>A, TCF1:c.1460G>A, TCF1:c.1375C>T, TCF1:c.1720A>G, TCF1:c.336G>A	1

From Illumina Laboratory Services, Illumina, SCV000376722.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	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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