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Variant: NM_000545.6(HNF1A):c.814C>T (p.Arg272Cys)

CA386966363

447503 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 0f1ff5b2-ff32-42cb-adcd-bc25b95b14cf
Approved on: 2022-04-15
Published on: 2022-04-15

HGVS expressions

NM_000545.6:c.814C>T
NM_000545.6(HNF1A):c.814C>T (p.Arg272Cys)
NC_000012.12:g.120994264C>T
CM000674.2:g.120994264C>T
NC_000012.11:g.121432067C>T
CM000674.1:g.121432067C>T
NC_000012.10:g.119916450C>T
NG_011731.2:g.20519C>T
ENST00000257555.11:c.814C>T
ENST00000257555.10:c.814C>T
ENST00000400024.6:c.814C>T
ENST00000402929.5:n.949C>T
ENST00000535955.5:n.43-3227C>T
ENST00000538626.2:n.191-3227C>T
ENST00000538646.5:c.627C>T
ENST00000540108.1:c.*254C>T
ENST00000541395.5:c.814C>T
ENST00000541924.5:c.713+558C>T
ENST00000543427.5:c.633+638C>T
ENST00000544413.2:c.814C>T
ENST00000544574.5:c.73-2353C>T
ENST00000560968.5:n.893+64C>T
ENST00000615446.4:c.-257-1998C>T
ENST00000617366.4:c.586+685C>T
NM_000545.5:c.814C>T
NM_001306179.1:c.814C>T
NM_000545.8:c.814C>T
NM_001306179.2:c.814C>T
NM_000545.8(HNF1A):c.814C>T (p.Arg272Cys)
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Pathogenic

Met criteria codes 8
PP4_Moderate PS4 PM1 PM5 PP3 PP1_Strong PM2_Supporting PS3_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.814C>T variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of arginine to cystine at codon 272 (p.(Arg272Cys) of transcript, e.g. NM_000545.8. This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1) and is absent from gnomAD v2.1.1 (PM2_Supporting). Additionally, this variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.941, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant was identified in at least 17 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4; PMIDs: 18003757, 28701371, 25414397, 11719843, 10447526; internal lab contributors). The variant segregated with diabetes, with at least fifteen informative meioses in at least sixteen families with MODY (PP1_Strong; internal lab contributors). Another missense variant, c. 815G>A, p.Arg272His, has been interpreted as pathogenic by the ClinGen MDEP and p.Arg272Cys has a greater Grantham distance (PM5). Functional studies demonstrated the p.Arg272Cys protein has DNA binding below 40% of wild type and transactivation below 40% of wildtype, indicating that this variant impacts protein function (PS3_Supporting; PMID: 10333057). Lastly, this variant was identified in at least five 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 sulfonylurea) (PP4_Moderate; internal lab contributors). In summary, c.814C>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, PM2_Supporting, PP3, PS4, PP1_Strong, PM5, PS3_Supporting, PP4_Moderate.
Met criteria codes
PP4_Moderate
The variant was identified in multiple individuals with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative HNF4A testing, and sulfonylurea-sensitive).
PS4
This variant was identified in at least 17 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes.
PM1
This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP.
PM5
Another missense variant, c.815G>A (p.Arg272His), has been interpreted as pathogenic by the ClinGen MDEP, and p.Arg272Cys has a greater Grantham distance.
PP3
REVEL 0.941 + FATHMM, LRT, MetaLR, MetaSVM, MutationTaster, PROVEAN and SIFT all predict deleterious; MutationAssessor said low, GERP score 4.84
PP1_Strong
This variant segregated with disease with 15 informative meioses in multiple families with MODY.
PM2_Supporting
Absent from gnomAD.
PS3_Supporting
Functional in vitro studies demonstrated that cells with this variant had no transactivation or DNA binding activity.
Curation History
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