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_001306179.1:c.710A>G

CA386965461

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 67e9416b-ce50-4afe-a22b-1f593fc64a58
Approved on: 2022-04-12
Published on: 2022-07-12

HGVS expressions

NM_001306179.1:c.710A>G
NC_000012.12:g.120993703A>G
CM000674.2:g.120993703A>G
NC_000012.11:g.121431506A>G
CM000674.1:g.121431506A>G
NC_000012.10:g.119915889A>G
NG_011731.2:g.19958A>G
ENST00000257555.11:c.710A>G
ENST00000257555.10:c.710A>G
ENST00000400024.6:c.710A>G
ENST00000402929.5:n.845A>G
ENST00000535955.5:n.43-3788A>G
ENST00000538626.2:n.191-3788A>G
ENST00000538646.5:c.527-461A>G
ENST00000540108.1:c.*150A>G
ENST00000541395.5:c.710A>G
ENST00000541924.5:c.710A>G
ENST00000543427.5:c.633+77A>G
ENST00000544413.2:c.710A>G
ENST00000544574.5:c.73-2914A>G
ENST00000560968.5:n.853A>G
ENST00000615446.4:c.-257-2559A>G
ENST00000617366.4:c.586+124A>G
NM_000545.5:c.710A>G
NM_000545.6:c.710A>G
NM_000545.8:c.710A>G
NM_001306179.2:c.710A>G

Likely Pathogenic

Met criteria codes 5
PP4_Moderate PM5_Supporting PM2_Supporting PM1_Supporting PP3
Not Met criteria codes 1
PS4

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.710A>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of asparagine to serine at codon 237 (p.(Asn273Ser)) 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 predicted to be deleterious by computational evidence, with a REVEL score of 0.706, which is greater than the MDEP VCEP threshold of 0.70 (PP3) and is absent from gnomAD v2.1.1 (PM2_Supporting). Another missense variant, c.709A>G (p.Asn237Asp) has been classified as likely pathogenic by the ClinGen MDEP (PM5_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, and response to low-dose sulfonylurea) (PP4_Moderate; internal lab contributors). This variant was identified in three unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors). In summary, c.710A>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/21): PM1_Supporting, PM2_Supporting, PP4_Moderate, PM5_Supporting, PP3.
Met criteria codes
PP4_Moderate
This variant was identified in two individuals with a clinical history suggestive of HNF1A-MODY (MODY probability calculator result >50% and negative genetic testing for HNF4A), one of whom also responded to low dose sulfonylurea treatment.
PM5_Supporting
The p.Asn237Asp variant has been interpreted as likely pathogenic by the MDEP.
PM2_Supporting
This variant is absent from gnomAD.
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.
PP3
REVEL 0.706 + FATHMM, LRT, MetaLR, MetaSVM, MutationTaster, PROVEAN and SIFT all predict deleterious; MutationAssessor said Medium, GERP score 4.45​
Not Met criteria codes
PS4
This variant was identified in three unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal lab contributors).
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.