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Variant: NM_001306179.2:c.675del

CA2580611076

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: b052e6b1-a258-47a4-adb0-21261027cd4a

HGVS expressions

NM_001306179.2:c.675del
NC_000012.12:g.120993668del
CM000674.2:g.120993668del
NC_000012.11:g.121431471del
CM000674.1:g.121431471del
NC_000012.10:g.119915854del
NG_011731.2:g.19923del
ENST00000257555.11:c.675del
ENST00000257555.10:c.675del
ENST00000400024.6:c.675del
ENST00000402929.5:n.810del
ENST00000535955.5:n.43-3823del
ENST00000538626.2:n.191-3823del
ENST00000538646.5:c.527-496del
ENST00000540108.1:c.*115del
ENST00000541395.5:c.675del
ENST00000541924.5:c.675del
ENST00000543427.5:c.633+42del
ENST00000544413.2:c.675del
ENST00000544574.5:c.73-2949del
ENST00000560968.5:c.818del
ENST00000615446.4:c.-257-2594del
ENST00000617366.4:c.586+89del
NM_000545.5:c.675del
NM_000545.6:c.675del
NM_001306179.1:c.675del
NM_000545.8:c.675del

Pathogenic

Met criteria codes 3
PM2_Supporting PVS1 PP1_Strong
Not Met criteria codes 2
PS4 PP4

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.675del variant in the HNF1 homeobox A gene, HNF1A, causes a frameshift in the protein at codon 225 (NM_000545.8), adding 8 novel amino acids before encountering a stop codon (p.(Ser225ArgfsTer8)). 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 at least two 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:11806470, PMID:33245425, PMID:1883825). One of the individuals and her sister had a phenotype suggestive of HNF1A-monogenic diabetes; however, the MODY probability was slightly below 50% and HNF4A was not evaluated, and PP4 could not be applied (PMID:11806470). This variant segregated with diabetes, with at least seven informative meioses in two families with MODY (PP1; PMID:11806470, PMID:33245425). In summary, c.675del 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, PP1_Strong, 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)
PP1_Strong
This variant segregated with diabetes, with at least seven informative meioses in two families with MODY (PP1; PMID:11806470, PMID:33245425).
Not Met criteria codes
PS4
This variant was identified in at least two 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:11806470, PMID:33245425, PMID:1883825).
PP4
This variant was identified in two related individuals with a phenotype suggestive of HNF1A-monogenic diabetes; however, the MODY probability was slightly below 50% and HNF4A was not evaluated (PMID:11806470).
Approved on: 2024-01-22
Published on: 2024-01-22
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