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
  • ClinVar Id was derived from the Allele Registry.


Variant: NM_001306179.2:c.382A>G

CA386959359

1327618 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 2ded1dde-214e-4617-b7cf-d03024b6036d

HGVS expressions

NM_001306179.2:c.382A>G
NC_000012.12:g.120988888A>G
CM000674.2:g.120988888A>G
NC_000012.11:g.121426691A>G
CM000674.1:g.121426691A>G
NC_000012.10:g.119911074A>G
NG_011731.2:g.15143A>G
ENST00000257555.11:c.382A>G
ENST00000257555.10:c.382A>G
ENST00000400024.6:c.382A>G
ENST00000402929.5:n.517A>G
ENST00000535955.5:n.43-8603A>G
ENST00000538626.2:n.191-8603A>G
ENST00000538646.5:c.382A>G
ENST00000540108.1:c.327-4632A>G
ENST00000541395.5:c.382A>G
ENST00000541924.5:c.382A>G
ENST00000543427.5:c.382A>G
ENST00000544413.2:c.382A>G
ENST00000544574.5:c.73-7729A>G
ENST00000560968.5:n.525A>G
ENST00000615446.4:c.-257-7374A>G
ENST00000617366.4:c.382A>G
NM_000545.5:c.382A>G
NM_000545.6:c.382A>G
NM_001306179.1:c.382A>G
NM_000545.8:c.382A>G
NM_000545.8(HNF1A):c.382A>G (p.Ile128Val)

Uncertain Significance

Met criteria codes 4
PM1_Supporting PP4_Moderate PP3 PM2_Supporting
Not Met criteria codes 2
PS4 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.382A>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of isoleucine to valine at codon 128 (p.(Ile128Val)) 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). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.7519, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and was identified in 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 (internal lab contributor). One of these individuals has a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and negative antibodies) (PP4_Moderate; internal lab contributor). This variant segregated with diabetes with one informative meiosis in their family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributor). In summary, c.382A>G meets the criteria to be classified as a variant of uncertain significance for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 6/4/2021): PP4_Moderate, PP3, PM1_Supporting, PM2_Supporting.
Met criteria codes
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).
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and negative antibodies) (PP4_Moderate; internal lab contributor).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.7519, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS4
This variant was identified in 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 (internal lab contributor).
PP1
This variant segregated with diabetes with one informative meiosis in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributor).
Approved on: 2021-12-09
Published on: 2022-07-11
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