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!


CA386965264

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: a8af1d7d-ca33-4f69-84b6-996c935a766a
Approved on: 2024-08-01
Published on: 2024-08-01

HGVS expressions

NM_001306179.2:c.694C>G
NC_000012.12:g.120993687C>G
CM000674.2:g.120993687C>G
NC_000012.11:g.121431490C>G
CM000674.1:g.121431490C>G
NC_000012.10:g.119915873C>G
NG_011731.2:g.19942C>G
ENST00000560968.6:c.694C>G
ENST00000257555.11:c.694C>G
ENST00000257555.10:c.694C>G
ENST00000400024.6:c.694C>G
ENST00000402929.5:n.829C>G
ENST00000535955.5:n.43-3804C>G
ENST00000538626.2:n.191-3804C>G
ENST00000538646.5:c.527-477C>G
ENST00000540108.1:c.*134C>G
ENST00000541395.5:c.694C>G
ENST00000541924.5:c.694C>G
ENST00000543427.5:c.633+61C>G
ENST00000544413.2:c.694C>G
ENST00000544574.5:c.73-2930C>G
ENST00000560968.5:c.837C>G
ENST00000615446.4:c.-257-2575C>G
ENST00000617366.4:c.586+108C>G
NM_000545.5:c.694C>G
NM_000545.6:c.694C>G
NM_001306179.1:c.694C>G
NM_000545.8:c.694C>G

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP1 PP4_Moderate PM1_Supporting PM5_Supporting
Not Met criteria codes 4
BP4 PS4 PS3 PP3

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.694C>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of leucine to valine at codon 232 (p.(Leu232Val)) 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) and is absent from gnomAD v2.1.1 (PM2_Supporting). This variant has a REVEL score of 0.688, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function. 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-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF4A) (PP4; internal lab contributors). This variant segregated with diabetes, with 3 informative meioses in 1 family (PP1; internal lab contributors). Another missense variant, c.695T>C p.Leu232Pro, has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). In summary, c.694C>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): PP4_Moderate, PP1, PM1_Supporting, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP1
This variant segregated with diabetes, with 3 informative meioses in 1 family (PP1; internal lab contributors).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for HNF1A-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF4A) (PP4; internal lab contributors).
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).
PM5_Supporting
Another missense variant, c.695T>C p.Leu232Pro, has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting).
Not Met criteria codes
BP4
This variant has a REVEL score of 0.688, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
PS4
Only 1 family found.
PS3
No studies found.
PP3
This variant has a REVEL score of 0.688, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
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