The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000545.8(HNF1A):c.388C>T (p.Gln130Ter)

CA386959398

994548 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: cfecfa50-3de4-48ee-9013-54f4336657ac

HGVS expressions

NM_000545.8:c.388C>T
NM_000545.8(HNF1A):c.388C>T (p.Gln130Ter)
NC_000012.12:g.120988894C>T
CM000674.2:g.120988894C>T
NC_000012.11:g.121426697C>T
CM000674.1:g.121426697C>T
NC_000012.10:g.119911080C>T
NG_011731.2:g.15149C>T
ENST00000560968.6:c.388C>T
ENST00000257555.11:c.388C>T
ENST00000257555.10:c.388C>T
ENST00000400024.6:c.388C>T
ENST00000402929.5:n.523C>T
ENST00000535955.5:n.43-8597C>T
ENST00000538626.2:n.191-8597C>T
ENST00000538646.5:c.388C>T
ENST00000540108.1:c.327-4626C>T
ENST00000541395.5:c.388C>T
ENST00000541924.5:c.388C>T
ENST00000543427.5:c.388C>T
ENST00000544413.2:c.388C>T
ENST00000544574.5:c.73-7723C>T
ENST00000560968.5:c.531C>T
ENST00000615446.4:c.-257-7368C>T
ENST00000617366.4:c.388C>T
NM_000545.5:c.388C>T
NM_000545.6:c.388C>T
NM_001306179.1:c.388C>T
NM_001306179.2:c.388C>T

Pathogenic

Met criteria codes 5
PVS1 PP1_Strong PS4_Moderate PM2_Supporting PP4_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 2.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.388C>T variant in the HNF1 homeobox A gene, HNF1A, results in a premature termination at codon 130 (p.(Gln130Ter)) of NM_000545.8. This variant, located in biologically-relevant exon 2 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 from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in seven unrelated (though part of a population isolate and likely having a common ancestor) individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors). This variant was segregated with diabetes, with eight informative meioses in four families with MODY (PP1_Strong; internal lab contributors). This variant was identified in at least 3 individuals with a clinical history highly specific for HNF1A-monogenic diabetes (MODY probability calculator result >75%, negative genetic testing for HNF4A, and negative antibodies) (PP4_Moderate; internal lab contributors). In summary, c.388C>T 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, PM2_supporting, PS4_moderate, PP1_strong, PP4_Moderate.
Met criteria codes
PVS1
This variant, located in biologically-relevant exon 2 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).
PP1_Strong
This variant was segregated with diabetes, with eight informative meioses in four families with MODY (PP1_Strong; internal lab contributors).
PS4_Moderate
This variant was identified in six unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting). gnomAD v4.0.0: absent
PP4_Moderate
This variant was identified in at least 3 individuals with a clinical history highly specific for HNF1A-monogenic diabetes (MODY probability calculator result >75%, negative genetic testing for HNF4A, and negative antibodies) (PP4_Moderate; internal lab contributors).
Approved on: 2024-06-09
Published on: 2024-06-09
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