The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000545.6(HNF1A):c.676_678del (p.Lys226del)

CA482164157

435428 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: e8311f88-3ca8-444e-86f3-43eee46c3167

HGVS expressions

NM_000545.6:c.676_678del
NM_000545.6(HNF1A):c.676_678del (p.Lys226del)
NC_000012.12:g.120993669_120993671del
CM000674.2:g.120993669_120993671del
NC_000012.11:g.121431472_121431474del
CM000674.1:g.121431472_121431474del
NC_000012.10:g.119915855_119915857del
NG_011731.2:g.19924_19926del
ENST00000257555.11:c.676_678del
ENST00000257555.10:c.676_678del
ENST00000400024.6:c.676_678del
ENST00000402929.5:n.811_813del
ENST00000535955.5:n.43-3822_43-3820del
ENST00000538626.2:n.191-3822_191-3820del
ENST00000538646.5:c.527-495_527-493del
ENST00000540108.1:c.*116_*118del
ENST00000541395.5:c.676_678del
ENST00000541924.5:c.676_678del
ENST00000543427.5:c.633+43_633+45del
ENST00000544413.2:c.676_678del
ENST00000544574.5:c.73-2948_73-2946del
ENST00000560968.5:n.819_821del
ENST00000615446.4:c.-257-2593_-257-2591del
ENST00000617366.4:c.586+90_586+92del
NM_000545.5:c.676_678del
NM_001306179.1:c.676_678del
NM_000545.8:c.676_678del
NM_001306179.2:c.676_678del
NM_000545.8(HNF1A):c.676_678del (p.Lys226del)

Uncertain Significance

Met criteria codes 4
PM4_Supporting PP4 PM2_Supporting PM1_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.676_678del variant in the HNF1 homeobox A gene, HNF1A, is a three base pair deletion resulting in the in-frame deletion of one amino acid at codon 226 (p.(Lys226del)) within exon 3 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). Additionally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). The c.676_678del variant is predicted to change the length of the protein due to an in-frame deletion of a single amino acid in a nonrepeat region (PM4_Supporting). Lastly, this variant was identified in an individual with a clinical history specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A) (PP4; internal lab contributors). In summary, c.676_678del 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 9/30/21): PM1_Supporting, PM2_Supporting, PM4_Supporting, PP4.
Met criteria codes
PM4_Supporting
The total protein length changes as a result of this single amino acid deletion in a nonrepeat region.
PP4
This variant was identified in an individual with a clinical history specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A) (internal lab contributors).
PM2_Supporting
This variant is absent from gnomAD.
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.
Approved on: 2022-04-11
Published on: 2022-07-12
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