The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: HNF1A vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000545.6(HNF1A):c.864del (p.Pro291fs)

CA6831842

435424 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: e26e934f-5188-4d08-8f32-c1fb50d132da
Approved on: 2025-06-09
Published on: 2025-06-09

HGVS expressions

NM_000545.6:c.864del
NM_000545.6(HNF1A):c.864del (p.Pro291fs)
NC_000012.12:g.120994314del
CM000674.2:g.120994314del
NC_000012.11:g.121432117del
CM000674.1:g.121432117del
NC_000012.10:g.119916500del
NG_011731.2:g.20569del
ENST00000560968.6:c.750+114del
ENST00000257555.11:c.864del
ENST00000257555.10:c.864del
ENST00000400024.6:c.864del
ENST00000402929.5:n.999del
ENST00000535955.5:n.43-3177del
ENST00000538626.2:n.191-3177del
ENST00000538646.5:c.677del
ENST00000540108.1:c.*304del
ENST00000541395.5:c.864del
ENST00000541924.5:c.713+608del
ENST00000543427.5:c.633+688del
ENST00000544413.2:c.864del
ENST00000544574.5:c.73-2303del
ENST00000560968.5:c.893+114del
ENST00000615446.4:c.-257-1948del
ENST00000617366.4:c.586+735del
NM_000545.5:c.864del
NM_001306179.1:c.864del
NM_000545.8:c.864del
NM_001306179.2:c.864del
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Likely Pathogenic

Met criteria codes 2
PVS1 PP4_Moderate
Not Met criteria codes 2
PS4 PM2

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.864del variant in the HNF1 homeobox A gene, HNF1A, causes a frameshift in the protein at codon 291 (NM_000545.8), adding 51 novel amino acids before encountering a stop codon (p.Pro291GlnfsTer51). 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). This variant was also identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and responded to low dose sulfonylureas) (PP4_Moderate; internal lab contributors). This variant failed QC in gnomAD and the frequency data is considered unreliable, therefore PM2_Supporting will not be applied. While this variant was identified in at least 7 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes, PS4_Moderate cannot be applied because the variant does not meet the PM2_Supporting (PMID: 26287533, internal lab contributors). In summary, c.864del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.1.0, approved 8/11/23): PVS1, PP4_Moderate
Met criteria codes
PVS1
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).
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 antibody negative and SU sensitive) (PP4_Moderate; internal lab contributors).
Not Met criteria codes
PS4
Cannot apply PS4 if PM2_Supporting is not applied.
PM2
The variant failed QC in gnomAD (Most of the carriers have low quality, only 4 carriers quality above 80, 2 above 90.
Curation History
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