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 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_000545.8(HNF1A):c.871C>A (p.Pro291Thr)

CA6831857

972814 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 08babbaa-0ebb-4af0-b035-ef9aa7c9f4ca
Approved on: 2025-09-26
Published on: 2025-09-26

HGVS expressions

NM_000545.8:c.871C>A
NM_000545.8(HNF1A):c.871C>A (p.Pro291Thr)
NC_000012.12:g.120994321C>A
CM000674.2:g.120994321C>A
NC_000012.11:g.121432124C>A
CM000674.1:g.121432124C>A
NC_000012.10:g.119916507C>A
NG_011731.2:g.20576C>A
ENST00000560968.6:c.750+121C>A
ENST00000257555.11:c.871C>A
ENST00000257555.10:c.871C>A
ENST00000400024.6:c.871C>A
ENST00000402929.5:n.1006C>A
ENST00000535955.5:n.43-3170C>A
ENST00000538626.2:n.191-3170C>A
ENST00000538646.5:c.684C>A
ENST00000540108.1:c.*311C>A
ENST00000541395.5:c.871C>A
ENST00000541924.5:c.713+615C>A
ENST00000543427.5:c.633+695C>A
ENST00000544413.2:c.871C>A
ENST00000544574.5:c.73-2296C>A
ENST00000560968.5:c.893+121C>A
ENST00000615446.4:c.-257-1941C>A
ENST00000617366.4:c.586+742C>A
NM_000545.5:c.871C>A
NM_000545.6:c.871C>A
NM_001306179.1:c.871C>A
NM_001306179.2:c.871C>A
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Uncertain Significance

Met criteria codes 2
PP4_Moderate PP1_Moderate
Not Met criteria codes 9
PM2 PM5 PM1 BS3 BS1 BP4 PS4 PS3 PP3

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 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.871C>A variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of proline to threonine at codon 291 (p.(Pro291Thr)) of NM_000545.8. The Grpmax filtering allele frequency of this variant in gnomAD v4.1.0 is 0.000017, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting and BS1; thus, neither criterion will be applied. This variant was identified in three unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4 cannot be applied because this number is below the ClinGen MDEP threshold and the variant has a MAF in gnomAD that is above the PM2_Supporting cutoff (PMIDs: 18003757, 30455330; internal lab contributors). This variant was identified in an individual with a clinical history highly specific for HNF1A-monogenic diabetes (>50% MODY probability calculator result and negative HNF4A testing; negative diabetes autoantibodies) (PP4_Moderate; internal lab contributors). This variant segregated with diabetes with three informative meioses in two families (PP1_Moderate; PMID: 22432108; internal lab contributors). This variant has a REVEL score of 0.587, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function. Functional studies of this variant are also inconclusive, as the variant results in transactivation activity 59.2% of WT, which falls between the cutoffs for PS3 and BS3. However, DNA binding activity and protein expression are not significantly different from WT (PMID: 18003757, Gloyn group)​. In summary, c.871C>A 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 3.0.0, approved 6/30/2025): PP1_moderate, PP4_moderate.
Met criteria codes
PP4_Moderate
This variant was identified in an individual with a clinical history highly specific for HNF1A-monogenic diabetes (>50% MODY probability calculator result and negative HNF4A testing; negative diabetes autoantibodies) (PP4_Moderate; internal lab contributors).
PP1_Moderate
This variant segregated with diabetes with three informative meioses in two families (PP1_Moderate; PMID: 22432108; internal lab contributors).
Not Met criteria codes
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No other variants at Pro291 are curated as pathogenic or likely pathogenic
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The Grpmax filtering allele frequency of this variant in gnomAD v4.1.0 is 0.000017, which falls between ClinGen MDEP-established cutoffs for PM2_Supporting and BS1; thus, neither criterion will be applied.
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant was identified in four unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4 cannot be applied because the variant has a Grpmax FAF in gnomAD that is above the PM2_Supporting cutoff (PMIDs: 18003757, 30455330; internal lab contributors).
PS3
Functional studies of this variant are inconclusive, as the variant results in transactivation activity 59.2% of WT, which falls between the cutoffs for PS3 and BS3. However, DNA binding activity and protein expression are not significantly different from WT (PMID: 18003757, Gloyn group)​
PP3
This variant has a REVEL score of 0.587, which is between the ClinGen MDEP thresholds for BP4 and PP3, predicting neither a damaging nor benign impact on HNF1A function.
Curation History
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