The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document


Variant: NM_001306179.2:c.397G>T

CA386959510

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: e34fe064-66ce-42d4-b075-c4e415ef419a

HGVS expressions

NM_001306179.2:c.397G>T
NC_000012.12:g.120988903G>T
CM000674.2:g.120988903G>T
NC_000012.11:g.121426706G>T
CM000674.1:g.121426706G>T
NC_000012.10:g.119911089G>T
NG_011731.2:g.15158G>T
ENST00000257555.11:c.397G>T
ENST00000257555.10:c.397G>T
ENST00000400024.6:c.397G>T
ENST00000402929.5:n.532G>T
ENST00000535955.5:n.43-8588G>T
ENST00000538626.2:n.191-8588G>T
ENST00000538646.5:c.397G>T
ENST00000540108.1:c.327-4617G>T
ENST00000541395.5:c.397G>T
ENST00000541924.5:c.397G>T
ENST00000543427.5:c.397G>T
ENST00000544413.2:c.397G>T
ENST00000544574.5:c.73-7714G>T
ENST00000560968.5:n.540G>T
ENST00000615446.4:c.-257-7359G>T
ENST00000617366.4:c.397G>T
NM_000545.5:c.397G>T
NM_000545.6:c.397G>T
NM_001306179.1:c.397G>T
NM_000545.8:c.397G>T

Uncertain Significance

Met criteria codes 5
PM5_Supporting PP4 PP3 PM2_Supporting PM1_Supporting
Not Met criteria codes 1
PP1

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.397G>T variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of valine to leucine at codon 133 (p.(Val133Leu)) of NM_000545.8. This variant is located within a conserved region of the DNA binding domain (codons 107-174 and 201-280) of HNF1A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.947, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and 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). This variant segregated with diabetes with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors). Another missense variant, c.397G>A (p.Val133Met), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting). In summary, c.397G>T 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 9/30/21): PP3, PP4, PM1_Supporting, PM2_Supporting, PM5_Supporting.
Met criteria codes
PM5_Supporting
Another missense variant, c.397G>A (p.Val133Met), has been classified as likely pathogenic by the ClinGen MDEP (PM5_Supporting).
PP4
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 contributor).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.947, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
PM1_Supporting
This variant is located within a conserved region of the DNA binding domain (codons 107-174 and 201-280) of HNF1A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting).
Not Met criteria codes
PP1
This variant segregated with diabetes with two informative meioses in a single family; however, this does not meet the thresholds for PP1 set by the ClinGen MDEP (PMID: 27236918, internal lab contributors).
Approved on: 2022-06-24
Published on: 2022-06-24
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