Variant: NM_001306179.2:c.427C>T

CA386959939

Gene: HNF1A

Condition: monogenic diabetes

Inheritance Mode: Autosomal dominant inheritance

UUID: 596cf859-5494-474e-8ffd-4f89b2dbe80a

HGVS expressions

NM_001306179.2:c.427C>T
NC_000012.12:g.120988933C>T
CM000674.2:g.120988933C>T
NC_000012.11:g.121426736C>T
CM000674.1:g.121426736C>T
NC_000012.10:g.119911119C>T
NG_011731.2:g.15188C>T
ENST00000257555.11:c.427C>T
ENST00000257555.10:c.427C>T
ENST00000400024.6:c.427C>T
ENST00000402929.5:n.562C>T
ENST00000535955.5:n.43-8558C>T
ENST00000538626.2:n.191-8558C>T
ENST00000538646.5:c.427C>T
ENST00000540108.1:c.327-4587C>T
ENST00000541395.5:c.427C>T
ENST00000541924.5:c.427C>T
ENST00000543427.5:c.427C>T
ENST00000544413.2:c.427C>T
ENST00000544574.5:c.73-7684C>T
ENST00000560968.5:n.570C>T
ENST00000615446.4:c.-257-7329C>T
ENST00000617366.4:c.427C>T
NM_000545.5:c.427C>T
NM_000545.6:c.427C>T
NM_001306179.1:c.427C>T
NM_000545.8:c.427C>T

Pathogenic

• Met criteria codes: PM1 PM2_Supporting PP4_Moderate PS4_Moderate PP1_Strong PP3

Expert Panel

Monogenic Diabetes VCEP

Criteria Specification Information

Evidence submitted by expert panel

Monogenic Diabetes VCEP

The c.427C>T variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of histidine to tyrosine at codon 143 (p.(His143Tyr)) of NM_000545.8. This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9639, which is greater than the MDEP threshold of 0.70 (PP3). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and was identified in 4 unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID: 10102714​, PMID: 9075819, PMID: 15928245, internal lab contributors). One of these individuals has a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and negative antibodies) (PP4_Moderate; internal lab contributor). This variant segregated with diabetes, with at least 8 informative meioses in one family with MODY (PP1_Strong; PMID 10102714/internal lab contributor). Taken together, this evidence supports the classification of this variant as pathogenic for monogenic diabetes. ACMG/AMP criteria applied as specified by the ClinGen MDEP VCEP (specification version 1.0, approved 8/24/21): PP1_Strong, PP4_moderate, PM1, PS4_moderate, PP3, PM2_Supporting.

Met criteria codes

• PM1: This variant resides in an amino acid within the HNF1α DNA binding domain that directly binds DNA, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1).
• PM2_Supporting: This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
• PP4_Moderate: 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, and negative antibodies) (PP4_Moderate; internal lab contributor).
• PS4_Moderate: This variant was identified in 4 unrelated individuals with non- autoimmune and non-absolute/near-absolute insulin-deficient diabetes (PS4_Moderate; PMID: 10102714​, PMID: 9075819, PMID: 15928245, internal lab contributors).
• PP1_Strong: This variant segregated with diabetes, with at least 8 informative meioses in one family with MODY (PP1_Strong; PMID 10102714/internal lab contributor).
• PP3: This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.9639, which is greater than the MDEP threshold of 0.70 (PP3).

Approved on: 2021-08-24

Published on: 2021-10-29