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.690_691del

CA2580611121

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 1206a6ce-fce4-4ea8-ae1f-a64bbccc60a6

HGVS expressions

NM_001306179.2:c.690_691del
NC_000012.12:g.120993683_120993684del
CM000674.2:g.120993683_120993684del
NC_000012.11:g.121431486_121431487del
CM000674.1:g.121431486_121431487del
NC_000012.10:g.119915869_119915870del
NG_011731.2:g.19938_19939del
ENST00000257555.11:c.690_691del
ENST00000257555.10:c.690_691del
ENST00000400024.6:c.690_691del
ENST00000402929.5:n.825_826del
ENST00000535955.5:n.43-3808_43-3807del
ENST00000538626.2:n.191-3808_191-3807del
ENST00000538646.5:c.527-481_527-480del
ENST00000540108.1:c.*130_*131del
ENST00000541395.5:c.690_691del
ENST00000541924.5:c.690_691del
ENST00000543427.5:c.633+57_633+58del
ENST00000544413.2:c.690_691del
ENST00000544574.5:c.73-2934_73-2933del
ENST00000560968.5:c.833_834del
ENST00000615446.4:c.-257-2579_-257-2578del
ENST00000617366.4:c.586+104_586+105del
NM_000545.5:c.690_691del
NM_000545.6:c.690_691del
NM_001306179.1:c.690_691del
NM_000545.8:c.690_691del

Pathogenic

Met criteria codes 5
PP1 PM2_Supporting PVS1 PP4_Moderate PS4_Moderate

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.690_691del variant in the HNF1 homeobox A gene, HNF1A, causes a frameshift in the protein at codon 230 NM_000545.8), adding 8 novel amino acids before encountering a stop codon (p.(p.Glu230AspfsTer8)). 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), and was identified in four unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID:18003757, internal lab contributors). At least two individuals have a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and antibody negative) (PP4_Moderate; internal lab contributor). This variant segregated with diabetes, with 3 informative meioses in a family with MODY (PP1; internal lab contributor). In summary, c.690_691del 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, approved 8/11/2023): PVS1, PP4_Moderate, PS4_Moderate, PP1, PM2_Supporting.
Met criteria codes
PP1
This variant segregated with diabetes, with 3 informative meioses in a family with MODY (PP1; internal lab contributor).
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 in at least two individuals with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and antibody negative) (PP4_Moderate; internal lab contributor).
PS4_Moderate
This variant was identified in four unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID:18003757, internal lab contributors).
Approved on: 2024-01-22
Published on: 2024-01-22
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