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_022895.3:c.*3089_*3099del

CA2580612120

Gene: C12orf43
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 014e9d84-899b-4b42-a119-07d21b2ed660
Approved on: 2024-10-13
Published on: 2024-10-13

HGVS expressions

NM_022895.3:c.*3089_*3099del
NC_000012.12:g.121001056_121001066del
CM000674.2:g.121001056_121001066del
NC_000012.11:g.121438859_121438869del
CM000674.1:g.121438859_121438869del
NC_000012.10:g.119923242_119923252del
NG_011731.2:g.27311_27321del
ENST00000560968.6:c.*516-9_*517del
ENST00000257555.11:c.1769-9_1770del
ENST00000257555.10:c.1769-9_1770del
ENST00000288757.7:c.*3089_*3099del
ENST00000540108.1:c.*1209-9_*1210del
ENST00000541395.5:c.1862-9_1863del
ENST00000543427.5:c.1232-9_1233del
ENST00000544413.2:c.1790-9_1791del
ENST00000560968.5:c.1586-9_1587del
ENST00000615446.4:c.557-9_558del
ENST00000617366.4:c.*178-9_*179del
NM_000545.5:c.1769-9_1770del
NM_000545.6:c.1769-9_1770del
NM_001306179.1:c.1790-9_1791del
NM_000545.8:c.1769-9_1770del
NM_001286191.2:c.*3089_*3099del
NM_001286196.2:c.*3089_*3099del
NM_001306179.2:c.1790-9_1791del
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Likely Pathogenic

Met criteria codes 3
PVS1_Strong 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.1769-9_1770del variant in the HNF1 homeobox A gene, HNF1A, is predicted to remove a splice acceptor site in intron 9 of NM_000545.8. Given the predicted loss of the intron 9 acceptor site, this variant is predicted to result in the loss of exon 10 and to disrupt a significant part of the transactivation domain, a functionally important region of the protein. Even though this truncated transcript is predicted to escape nonsense mediated decay in a gene in which loss-of-function is an established mechanism of disease, there is clinical evidence that variants in this region lead to a monogenic diabetes phenotype. (PVS1_Strong; PMID: 23348805). This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting). Additionally, 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, and sensitive to sulfonyureas) (PP4_Moderate; internal lab contributors). In summary, c.1769-9_1770del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.1, approved 8/11/2023): PVS1_Strong, PM2_Supporting, PP4_Moderate).
Met criteria codes
PVS1_Strong
This variant, predicted to result in loss of the intron 9 acceptor site and therefore the loss of exon 10, is predicted to disrupt a significant part of the transactivation domain, a functionally important region of the protein. Even though this truncated transcript is predicted to escape nonsense mediated decay in a gene in which loss-of-function is an established mechanism of disease, there is clinical evidence that variants in this region lead to a monogenic diabetes phenotype. (PVS1_Strong; PMID: 23348805).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 and v4.1 (PM2_Supporting).
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, and sensitive to sulfonyureas) (PP4_Moderate; internal lab contributors).
Curation History
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