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Variant: NM_000545.6(HNF1A):c.872dup (p.Gly292fs)

CA124453

14927 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: cde6fb52-5469-4017-b30d-60b5d552ef1f

HGVS expressions

NM_000545.6:c.872dup
NM_000545.6(HNF1A):c.872dup (p.Gly292fs)
NC_000012.12:g.120994322dup
CM000674.2:g.120994322dup
NC_000012.11:g.121432125dup
CM000674.1:g.121432125dup
NC_000012.10:g.119916508dup
NG_011731.2:g.20577dup
ENST00000257555.11:c.872dup
ENST00000257555.10:c.872dup
ENST00000400024.6:c.872dup
ENST00000402929.5:n.1007dup
ENST00000535955.5:n.43-3169dup
ENST00000538626.2:n.191-3169dup
ENST00000538646.5:c.685dup
ENST00000540108.1:c.*312dup
ENST00000541395.5:c.872dup
ENST00000541924.5:c.713+616dup
ENST00000543427.5:c.633+696dup
ENST00000544413.2:c.872dup
ENST00000544574.5:c.73-2295dup
ENST00000560968.5:n.893+122dup
ENST00000615446.4:c.-257-1940dup
ENST00000617366.4:c.586+743dup
NM_000545.5:c.872dup
NM_001306179.1:c.872dup
NM_000545.8:c.872dup
NM_001306179.2:c.872dup
NM_000545.8(HNF1A):c.872dup (p.Gly292fs)

Pathogenic

Met criteria codes 3
PS2_Moderate PVS1 PP1_Strong
Not Met criteria codes 2
PM2 PS4

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.872dupC variant in the HNF1 homeobox A gene, HNF1A, causes a frameshift in the protein at codon 292 (NM_000545.8), adding 25 novel amino acids before encountering a stop codon (p.(Gly292ArgfsTer25)). This variant, located in biologically-relevant exon 4 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). Additionally, this variant segregated with diabetes, with at least 100 informative meioses in multiple families with MODY (PP1_Strong; internal lab contributors). This variant was identified as a de novo occurrence with confirmed parental relationships in one individual and unconfirmed parental relationships in another individual with diabetes, but whose clinical picture is suggestive but not highly specific for HNF1A-MODY (MODY probability calculator result >50% but HNF4A not tested) (PS2_Moderate; PMID:9166684, internal lab contributors). The variant is located in a poly-C tract and failed QC in gnomAD v2.1.1 in a manner typical of single base deletions in poly-C tracts in NGS; therefore, PM2_Supporting could not be applied. This variant was identified in at least 200 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because PM2_Supporting cannot be applied (internal lab contributors). In summary, c.872dupC meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/21): PVS1, PS2_Moderate, PP1_Strong.
Met criteria codes
PS2_Moderate
This variant was found in two individuals with diabetes (MPC >50% but HNF4A not tested), one confirmed de novo and one assumed de novo (PMID: 9166684, internal lab contributor).
PVS1
This variant is predicted to cause loss of function by resulting in nonsense mediated decay of a biologically relevant transcript.
PP1_Strong
This variant segregated with disease with at least 100 informative meioses observed in multiple families with MODY (internal laboratory contributors).
Not Met criteria codes
PM2
Failed gnomAD QC.
PS4
This variant was identified in at least 200 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because the variant failed QC in gnomAD and it cannot be determined if PM2_Supporting applies (internal lab contributors). PS4 cannot be used if PM2_supporting does not apply.
Approved on: 2022-04-15
Published on: 2022-07-12
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