The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000545.8(HNF1A):c.335C>T (p.Pro112Leu)

CA124475

14942 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 53a9fce0-d78f-477d-9a67-dfcbda28884c
Approved on: 2022-04-08
Published on: 2022-07-12

HGVS expressions

NM_000545.8:c.335C>T
NM_000545.8(HNF1A):c.335C>T (p.Pro112Leu)
NC_000012.12:g.120988841C>T
CM000674.2:g.120988841C>T
NC_000012.11:g.121426644C>T
CM000674.1:g.121426644C>T
NC_000012.10:g.119911027C>T
NG_011731.2:g.15096C>T
ENST00000257555.11:c.335C>T
ENST00000257555.10:c.335C>T
ENST00000400024.6:c.335C>T
ENST00000402929.5:n.470C>T
ENST00000535955.5:n.43-8650C>T
ENST00000538626.2:n.191-8650C>T
ENST00000538646.5:c.335C>T
ENST00000540108.1:c.327-4679C>T
ENST00000541395.5:c.335C>T
ENST00000541924.5:c.335C>T
ENST00000543427.5:c.335C>T
ENST00000544413.2:c.335C>T
ENST00000544574.5:c.73-7776C>T
ENST00000560968.5:n.478C>T
ENST00000615446.4:c.-257-7421C>T
ENST00000617366.4:c.335C>T
NM_000545.5:c.335C>T
NM_000545.6:c.335C>T
NM_001306179.1:c.335C>T
NM_001306179.2:c.335C>T
More

Pathogenic

Met criteria codes 7
PP4_Moderate PS3 PM1 PP3 PS4_Moderate PP1_Strong PM2_Supporting

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.335C>T variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of proline to leucine at codon 112 (p.(Pro112Leu)) of NM_000545.8. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.966, which is greater than the MDEP VCEP threshold of 0.70 (PP3) and is absent from gnomAD v2.1.1 (PM2_Supporting). Additionally, 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 (PM1_Supporting). This variant was identified in six unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors). This variant was identified in two individuals with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and response to low dose sulfonylureas) (PP4_Moderate; internal lab contributors). A luciferase assay meeting the ClinGen MDEP quality control specifications demonstrated that the p.Pro112Leu protein has transactivation activity below 40% of wildtype, indicating that this variant impacts protein function (PS3_Moderate, PMID: 32910913). Lastly, this variant segregated with diabetes, with 11 informative meioses in six families with MODY (PP1_Strong; internal lab contributors). In summary, c.335C>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 9/30/21): PP3, PM1_Supporting, PM2_Supporting, PP4_Moderate, PS4_Moderate,PS3_Moderate, PP1_Strong.
Met criteria codes
PP4_Moderate
This variant was identified in two individuals with a clinical history highly significant HNF1A-MODY (MODY probability calculator result >50% and negative genetic testing for HNF4A), who also responded to low dose sulfonylureas.
PS3
Two functional in vitro studies demonstrated that cells with this variant display decreased transactivation and DNA binding (both <40% compared to wild type), but do retain normal cellular localization (PMIDs: 27899486 and 12574234).
PM1
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/
PP3
REVEL 0.966+ FATHMM, LRT, MetaLR, MetaSVM, MutationTaster, PROVEAN and SIFT all predict deleterious; MutationAssessor said Medium, GERP score 5.08
PS4_Moderate
This variant was identified in six unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors).
PP1_Strong
This variant segregated with disease in 11 informative meioses in six families with MODY (internal lab contributors).
PM2_Supporting
This variant has a minor allele frequency in gnomAD of less than 0.00002 in the European non-Finnish sub-population (actual value = 0.000008803) and is absent from other gnomAD sub-populations.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.