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

  • See Evidence submitted by expert panel for details.

Variant: NM_000545.8(HNF1A):c.871C>G (p.Pro291Ala)

CA244533124

1334146 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: cc7e31c6-cc9d-4bcf-8be8-1ccd9fa74a69

HGVS expressions

NM_000545.8:c.871C>G
NM_000545.8(HNF1A):c.871C>G (p.Pro291Ala)
NC_000012.12:g.120994321C>G
CM000674.2:g.120994321C>G
NC_000012.11:g.121432124C>G
CM000674.1:g.121432124C>G
NC_000012.10:g.119916507C>G
NG_011731.2:g.20576C>G
ENST00000257555.11:c.871C>G
ENST00000257555.10:c.871C>G
ENST00000400024.6:c.871C>G
ENST00000402929.5:n.1006C>G
ENST00000535955.5:n.43-3170C>G
ENST00000538626.2:n.191-3170C>G
ENST00000538646.5:c.684C>G
ENST00000540108.1:c.*311C>G
ENST00000541395.5:c.871C>G
ENST00000541924.5:c.713+615C>G
ENST00000543427.5:c.633+695C>G
ENST00000544413.2:c.871C>G
ENST00000544574.5:c.73-2296C>G
ENST00000560968.5:n.893+121C>G
ENST00000615446.4:c.-257-1941C>G
ENST00000617366.4:c.586+742C>G
NM_000545.5:c.871C>G
NM_000545.6:c.871C>G
NM_001306179.1:c.871C>G
NM_001306179.2:c.871C>G

Uncertain Significance

Met criteria codes 5
PM2_Supporting BS2 BP2 PS4_Moderate PP4
Not Met criteria codes 3
BP5 PP3 PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.871C>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of proline to alanine at codon 291 (p.(Pro291Ala)) of NM_000545.8. This variant was identified in 4 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; internal lab contributors). Also, this variant has a minor allele frequency of 0.000009234 in the gnomAD v2.1.1 European non-Finnish population which is less than the ClinGen MDEP threshold for PM2_Supporting (≤0.00002 and ≤1 copy in any other subpopulation) (PM2_Supporting). 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) (PP4; internal lab contributors). Additionally, this variant was identified in a patient with different HNF1A variant curated by MDEP as pathogenic (BP2; internal lab contributors). This variant was identified in a normoglycemic individual >70 years old, and the expected penetrance for HNF1A-MODY is 95% by age 70 (BS2; internal lab contributors). This variant has a REVEL score of 0.28, which is between the ClinGen MDEP thresholds, predicting neither a damaging nor benign impact on HNF1A function. In summary, c.871C>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 9/30/2021): PS4_Moderate, PM2_Supporting, PP4, BP5, BS2
Met criteria codes
PM2_Supporting
gnomAD v2.1 MAF 0.000009234 in gnomAD ENF (1 allele)
BS2
Normoglycemic individual >70 years old
BP2
Individual tested in clinical laboratory found to have other pathogenic variant in HNF1A
PS4_Moderate
4 cases: One from a clinical laboratory, two cases affected with DM in a large biobank, and one case in the Paris database
PP4
MPC >50% at diagnosis, MPC <50% currently but negative antibodies. Using PP4 at supporting level.
Not Met criteria codes
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL 0.28
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-04-21
Published on: 2022-04-21
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.