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
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_001306179.2:c.395A>T

CA386959470

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 67860509-33fd-49ea-b96a-0de079e0f05c

HGVS expressions

NM_001306179.2:c.395A>T
NC_000012.12:g.120988901A>T
CM000674.2:g.120988901A>T
NC_000012.11:g.121426704A>T
CM000674.1:g.121426704A>T
NC_000012.10:g.119911087A>T
NG_011731.2:g.15156A>T
ENST00000560968.6:c.395A>T
ENST00000257555.11:c.395A>T
ENST00000257555.10:c.395A>T
ENST00000400024.6:c.395A>T
ENST00000402929.5:n.530A>T
ENST00000535955.5:n.43-8590A>T
ENST00000538626.2:n.191-8590A>T
ENST00000538646.5:c.395A>T
ENST00000540108.1:c.327-4619A>T
ENST00000541395.5:c.395A>T
ENST00000541924.5:c.395A>T
ENST00000543427.5:c.395A>T
ENST00000544413.2:c.395A>T
ENST00000544574.5:c.73-7716A>T
ENST00000560968.5:c.538A>T
ENST00000615446.4:c.-257-7361A>T
ENST00000617366.4:c.395A>T
NM_000545.5:c.395A>T
NM_000545.6:c.395A>T
NM_001306179.1:c.395A>T
NM_000545.8:c.395A>T

Likely Pathogenic

Met criteria codes 5
PP4 PP3 PM5 PM1 PM2_Supporting

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.395A>T variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of glutamic acid to valine at codon 132 (p.(Glu132Val)) of NM_000545.8. This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.93, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result nearly 50%, negative genetic testing for HNF4A, negative antibodies, and 3 generation family history of diabetes) (PP4; internal lab contributors). Another missense variant, c.394G>A p.Glu132Lys, has been classified as pathogenic by the ClinGen MDEP, and p.Glu132Asp has a greater Grantham distance. In summary, c.395A>T 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): PM1, PM5, PP3, PP4, PM2_Supporting.
Met criteria codes
PP4
This variant was identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result nearly 50%, negative genetic testing for HNF4A, negative antibodies, and 3 generation family history of diabetes) (PP4; internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.93, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PM5
Another missense variant, c.394G>A p.Glu132Lys, has been classified as pathogenic by the ClinGen MDEP, and p.Glu132Asp has a greater Grantham distance (PM5_Supporting). Glu-Lys: 56 Glu-Val: 121
PM1
This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Absent from gnomAD 4.1
Approved on: 2024-06-09
Published on: 2024-06-09
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