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.682dup

CA2580611120

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 87a7a524-5640-4ec5-b6ed-79a36a66fccf

HGVS expressions

NM_001306179.2:c.682dup
NC_000012.12:g.120993675dup
CM000674.2:g.120993675dup
NC_000012.11:g.121431478dup
CM000674.1:g.121431478dup
NC_000012.10:g.119915861dup
NG_011731.2:g.19930dup
ENST00000257555.11:c.682dup
ENST00000257555.10:c.682dup
ENST00000400024.6:c.682dup
ENST00000402929.5:n.817dup
ENST00000535955.5:n.43-3816dup
ENST00000538626.2:n.191-3816dup
ENST00000538646.5:c.527-489dup
ENST00000540108.1:c.*122dup
ENST00000541395.5:c.682dup
ENST00000541924.5:c.682dup
ENST00000543427.5:c.633+49dup
ENST00000544413.2:c.682dup
ENST00000544574.5:c.73-2942dup
ENST00000560968.5:c.825dup
ENST00000615446.4:c.-257-2587dup
ENST00000617366.4:c.586+96dup
NM_000545.5:c.682dup
NM_000545.6:c.682dup
NM_001306179.1:c.682dup
NM_000545.8:c.682dup

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP4_Moderate
Not Met criteria codes 2
PS4 PP1

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.682dup variant in the HNF1 homebox A gene, HNF1A, causes a frameshift in the protein at codon 228 (NM_000545.8), adding 11 novel amino acids before encountering a stop codon (p.(Glu228GlyfsTer11)). This variant, located in biologically-relevant exon 3 of 10, is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 23348805). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in three 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 contributor). One of these individuals had a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4Al, and negative antibodies) (PP4; internal lab contributor). This variant segregated with diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributor). In summary, c.682dup meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.0, approved 8/11/2023): PVS1, PP4_Moderate, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PVS1
This variant, located in biologically-relevant exon 3 of 10, is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 23348805).
PP4_Moderate
This variant was identified 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).
Not Met criteria codes
PS4
This variant was identified in three 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 contributor).
PP1
This variant segregated with diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributor).
Approved on: 2024-01-22
Published on: 2024-01-22
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