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Variant: NM_000545.6(HNF1A):c.827C>G (p.Ala276Gly)

CA214333

36832 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: dd260f0c-2bdd-436f-a826-303719f78af1

HGVS expressions

NM_000545.6:c.827C>G
NM_000545.6(HNF1A):c.827C>G (p.Ala276Gly)
NC_000012.12:g.120994277C>G
CM000674.2:g.120994277C>G
NC_000012.11:g.121432080C>G
CM000674.1:g.121432080C>G
NC_000012.10:g.119916463C>G
NG_011731.2:g.20532C>G
ENST00000257555.11:c.827C>G
ENST00000257555.10:c.827C>G
ENST00000400024.6:c.827C>G
ENST00000402929.5:n.962C>G
ENST00000535955.5:n.43-3214C>G
ENST00000538626.2:n.191-3214C>G
ENST00000538646.5:c.640C>G
ENST00000540108.1:c.*267C>G
ENST00000541395.5:c.827C>G
ENST00000541924.5:c.713+571C>G
ENST00000543427.5:c.633+651C>G
ENST00000544413.2:c.827C>G
ENST00000544574.5:c.73-2340C>G
ENST00000560968.5:n.893+77C>G
ENST00000615446.4:c.-257-1985C>G
ENST00000617366.4:c.586+698C>G
NM_000545.5:c.827C>G
NM_001306179.1:c.827C>G
NM_000545.8:c.827C>G
NM_001306179.2:c.827C>G
NM_000545.8(HNF1A):c.827C>G (p.Ala276Gly)

Likely Pathogenic

Met criteria codes 6
PM1_Supporting PS4_Moderate PM2_Supporting PM5_Supporting PP3 PP4_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.827C>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of alanine to glycine at codon 276 (p.(Ala276Gly)) of NM_000545.8. 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 also is predicted to be deleterious by computational evidence, with a REVEL score of 0.901, which is greater than the MDEP VCEP threshold of 0.70 (PP3). Additionally, this variant has a minor allele frequency of 0.000007816 in the gnomAD v2.1.1 European non-Finnish population and one copy in another subpopulation, which is less than the ClinGen MDEP threshold for PM2_Supporting (≤0.00002 and ≤1 copy in any other subpopulation) (PM2_Supporting). This variant was identified in 6 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors). At least one of these individuals had 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 sulfonylureas) (PP4_Moderate; internal lab contributor). Another missense variant, c.827C>A (p.Ala276Asp), has been classified as pathogenic by the ClinGen MDEP but has a greater Grantham distance than p.Ala276Gly (PM5_Supporting). In summary, c.827C>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/2021): PM1_Supporting, PP3, PM2_Supporting, PS4_Moderate, PP4_Moderate, PM5_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.
PS4_Moderate
This variant was identified in six unrelated individuals with a clinical picture consistent with monogenic diabetes (internal laboratory contributors).
PM2_Supporting
This variant has a minor allele frequency in gnomAD of less than 0.00002 in the European non-Finnish population (actual value = 0.000007816) and only one allele is present in the African population.
PM5_Supporting
Another missense variant, c.827C>A (p.Ala276Asp) has been classified as Pathogenic by the ClinGen MDEP (LP without PM5_Supporting based on this one; also p.Ala276Asp has greater GD).
PP3
This variant is predicted to be deleterious by multiple lines of computational evidence with a REVEL score of 0.901.
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, sulfonylurea-sensitive, and antibody negative) (PP4_Moderate; internal lab contributors).
Approved on: 2022-05-03
Published on: 2022-05-03
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