The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document


Variant: NM_001306179.2:c.676A>G

CA386965032

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: f41bb4ec-10c2-410a-97fe-831a9496c951

HGVS expressions

NM_001306179.2:c.676A>G
NC_000012.12:g.120993669A>G
CM000674.2:g.120993669A>G
NC_000012.11:g.121431472A>G
CM000674.1:g.121431472A>G
NC_000012.10:g.119915855A>G
NG_011731.2:g.19924A>G
ENST00000257555.11:c.676A>G
ENST00000257555.10:c.676A>G
ENST00000400024.6:c.676A>G
ENST00000402929.5:n.811A>G
ENST00000535955.5:n.43-3822A>G
ENST00000538626.2:n.191-3822A>G
ENST00000538646.5:c.527-495A>G
ENST00000540108.1:c.*116A>G
ENST00000541395.5:c.676A>G
ENST00000541924.5:c.676A>G
ENST00000543427.5:c.633+43A>G
ENST00000544413.2:c.676A>G
ENST00000544574.5:c.73-2948A>G
ENST00000560968.5:c.819A>G
ENST00000615446.4:c.-257-2593A>G
ENST00000617366.4:c.586+90A>G
NM_000545.5:c.676A>G
NM_000545.6:c.676A>G
NM_001306179.1:c.676A>G
NM_000545.8:c.676A>G

Likely Pathogenic

Met criteria codes 5
PP4_Moderate PM2_Supporting PM1_Supporting PP1_Strong PP3
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for HNF1A Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.676A>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of lysine to glutamic acid at codon 226 (p.(Lys226Glu)) 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 is predicted to be deleterious by computational evidence, with a REVEL score of 0.815, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting), and identified in two unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID:18003757, internal lab contributors). One individual has a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and negative antibodies) (PP4_Moderate; internal lab contributor). This variant segregated with diabetes, with at least four informative meioses in two families with MODY (PP1_Strong; internal lab contributors). In summary, c.676A>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 2.1.0, approved 8/11/2023): PP1_Strong, PP4_Moderate, PP3, PM1_Supporting, PM2_Supporting.
Met criteria codes
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, and negative antibodies) (PP4_Moderate; internal lab contributor).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
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 (PM1_Supporting).
PP1_Strong
This variant segregated with diabetes, with at least four informative meioses in two families with MODY (PP1_Strong; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.815, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
Not Met criteria codes
PS4
This variant was identified in two unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (PMID:18003757, internal lab contributors).
Approved on: 2024-01-22
Published on: 2024-01-22
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