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Variant: NM_000545.8(HNF1A):c.827C>A (p.Ala276Asp)

CA124481

14945 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: b1ec8b81-961e-47de-94da-be293288ac39

HGVS expressions

NM_000545.8:c.827C>A
NM_000545.8(HNF1A):c.827C>A (p.Ala276Asp)
NC_000012.12:g.120994277C>A
CM000674.2:g.120994277C>A
NC_000012.11:g.121432080C>A
CM000674.1:g.121432080C>A
NC_000012.10:g.119916463C>A
NG_011731.2:g.20532C>A
ENST00000257555.11:c.827C>A
ENST00000257555.10:c.827C>A
ENST00000400024.6:c.827C>A
ENST00000402929.5:n.962C>A
ENST00000535955.5:n.43-3214C>A
ENST00000538626.2:n.191-3214C>A
ENST00000538646.5:c.640C>A
ENST00000540108.1:c.*267C>A
ENST00000541395.5:c.827C>A
ENST00000541924.5:c.713+571C>A
ENST00000543427.5:c.633+651C>A
ENST00000544413.2:c.827C>A
ENST00000544574.5:c.73-2340C>A
ENST00000560968.5:n.893+77C>A
ENST00000615446.4:c.-257-1985C>A
ENST00000617366.4:c.586+698C>A
NM_000545.5:c.827C>A
NM_000545.6:c.827C>A
NM_001306179.1:c.827C>A
NM_001306179.2:c.827C>A

Pathogenic

Met criteria codes 6
PM1_Supporting PP3 PS3_Supporting PP4_Moderate PM5_Supporting PP1_Strong
Not Met criteria codes 2
PS4 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.827C>A variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of alanine to aspartic acid at codon 276 (p.(Ala276Asp)) 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, 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 two individuals with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, antibody-negative, and response to low-dose sulfonylurea (PP4_Moderate, internal lab contributors). Another missense variant, c.827C>G (p.Ala276Gly), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). Also, the variant segregated with diabetes, with four informative meioses in two families with MODY (PP1_Strong; internal lab contributors). Functional studies demonstrated abnormal nuclear localization, DNA binding less than 40% of wildtype, and normal transactivation (PS3_Supporting; PMID:12574234). This variant is absent from the gnomAD European non-Finnish population, but two copies are present in the African population; therefore PM2_Supporting cannot be applied. This variant was identified in at least 12 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4 cannot be applied because the variant MAF in gnomAD is above the ClinGen MDEP PM2_Supporting cutoff (PMID: 12574234, internal lab contributors). In summary, c.827C>A 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): PP1_Strong, PP4_Moderate, PP3, PM1_Supporting, PM5_Supporting, PS3_Supporting.
Met criteria codes
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.
PP3
REVEL 0.956 + GERP, FATHMM, LRT, MetaLR, MetaSVM, MutationAssessor, MutationTaster, PROVEAN and SIFT all predict deleterious
PS3_Supporting
Functional studies demonstrated abnormal nuclear localization, DNA binding 30% of WT, and normal transactivational activity (no correlation between DNA binding and transactivation activity).
PP4_Moderate
This variant was identified in two individuals with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result of greater than 50%, negative genetic testing for HNF4A, antibody negative, and sulfonylurea-sensitive).
PM5_Supporting
The p.Ala276Gly variant has been interpreted as likely pathogenic by the MDEP.
PP1_Strong
This variant segregated with diabetes, with four informative meioses in two families with MODY (internal lab contributors).
Not Met criteria codes
PS4
This variant was identified in at least 12 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4 cannot be applied because the variant MAF in gnomAD is above the ClinGen MDEP PM2_Supporting cutoff (PMID: 12574234, internal lab contributors).
PM2
This variant is absent from the gnomAD European non-Finnish population, but two copies are present in the African population.
Approved on: 2022-04-18
Published on: 2022-04-18
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