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Variant: NM_000545.6(HNF1A):c.779C>T (p.Thr260Met)

CA10588543

265436 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: b5943d8b-4ba3-402c-879f-9049fe2f8a98

HGVS expressions

NM_000545.6:c.779C>T
NM_000545.6(HNF1A):c.779C>T (p.Thr260Met)
NC_000012.12:g.120994229C>T
CM000674.2:g.120994229C>T
NC_000012.11:g.121432032C>T
CM000674.1:g.121432032C>T
NC_000012.10:g.119916415C>T
NG_011731.2:g.20484C>T
ENST00000257555.11:c.779C>T
ENST00000257555.10:c.779C>T
ENST00000400024.6:c.779C>T
ENST00000402929.5:n.914C>T
ENST00000535955.5:n.43-3262C>T
ENST00000538626.2:n.191-3262C>T
ENST00000538646.5:c.592C>T
ENST00000540108.1:c.*219C>T
ENST00000541395.5:c.779C>T
ENST00000541924.5:c.713+523C>T
ENST00000543427.5:c.633+603C>T
ENST00000544413.2:c.779C>T
ENST00000544574.5:c.73-2388C>T
ENST00000560968.5:n.893+29C>T
ENST00000615446.4:c.-257-2033C>T
ENST00000617366.4:c.586+650C>T
NM_000545.5:c.779C>T
NM_001306179.1:c.779C>T
NM_000545.8:c.779C>T
NM_001306179.2:c.779C>T
NM_000545.8(HNF1A):c.779C>T (p.Thr260Met)

Pathogenic

Met criteria codes 7
PS3_Moderate PS4 PP1_Strong PM1_Supporting PM2_Supporting PP3 PP4_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.779C>T variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of threonine to methionine at codon 260 (p.(Thr260Met)) of NM_000545.8. This variant is located within a conserved region of the DNA binding domain (107-174 and 201-280) of HNF1A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting). Additionally, variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.956, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in at least 28 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PMIDs: 30760653, 29927023, 30663027, 29207974, 28105082, internal lab contributors). At least two of these individuals had a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50% and negative genetic testing for HNF4A, and both were antibody negative and one responded to low dose sulfonylureas) (PP4_Moderate; PMIDs: 30760653, 281505082). This variant segregated with diabetes, with 16 informative meioses in multiple families with MODY (PP1_Strong; PMIDs: 30760653. 28105082, internal lab contributors). A luciferase assay meeting the ClinGen MDEP quality control specifications demonstrated that the p.Thr260Met protein has transactivation activity below 40% of wildtype, indicating that this variant impacts protein function (PS3_Moderate; PMID: 32910913). In summary, c.779C>T meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/2021): PM1_supporting, PM2_Supporting, PP3, PS4, PP4_Moderate, PP1_Strong, PS3_Moderate.
Met criteria codes
PS3_Moderate
A luciferase assay meeting the ClinGen MDEP quality control specifications demonstrated that the p.Thr260Met protein has transactivation activity below 40% of wildtype, indicating that this variant impacts protein function (PMID: 32910913).
PS4
This variant was identified in at least 28 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes.
PP1_Strong
This variant segregated with diabetes, with 16 informative meioses in multiple families with MODY (PP1_Strong; PMIDs: 30760653. 28105082, internal lab contributors).
PM1_Supporting
This variant is located within a conserved region of the DNA binding domain (codons 107-174 and 201-280) of HNF1A, which is defined as critical for the protein’s function by the ClinGen MDEP.
PM2_Supporting
This variant is absent from gnomAD European non-Finnish population, and only one copy is present in the East Asian population.
PP3
REVEL 0.956 + FATHMM, LRT, MetaLR, MetaSVM, MutationTaster, PROVEAN and SIFT all predict deleterious; MutationAssessor said Medium, GERP score 4.84
PP4_Moderate
This variant was identified in two individuals with a clinical history suggestive of HNF1A-MODY (MODY probability calculator result >50% and negative genetic testing for HNF4A), and both were antibody negative and one responded to low dose sulfonylureas.
Approved on: 2022-04-14
Published on: 2022-07-12
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