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
  • ClinVar Id was derived from the Allele Registry.


Variant: NM_001306179.2:c.737T>G

CA386965868

1173962 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 2e3744dd-9da4-4a59-acb0-ad7e6d3ad870

HGVS expressions

NM_001306179.2:c.737T>G
NC_000012.12:g.120994187T>G
CM000674.2:g.120994187T>G
NC_000012.11:g.121431990T>G
CM000674.1:g.121431990T>G
NC_000012.10:g.119916373T>G
NG_011731.2:g.20442T>G
ENST00000257555.11:c.737T>G
ENST00000257555.10:c.737T>G
ENST00000400024.6:c.737T>G
ENST00000402929.5:n.872T>G
ENST00000535955.5:n.43-3304T>G
ENST00000538626.2:n.191-3304T>G
ENST00000538646.5:c.550T>G
ENST00000540108.1:c.*177T>G
ENST00000541395.5:c.737T>G
ENST00000541924.5:c.713+481T>G
ENST00000543427.5:c.633+561T>G
ENST00000544413.2:c.737T>G
ENST00000544574.5:c.73-2430T>G
ENST00000560968.5:n.880T>G
ENST00000615446.4:c.-257-2075T>G
ENST00000617366.4:c.586+608T>G
NM_000545.5:c.737T>G
NM_000545.6:c.737T>G
NM_001306179.1:c.737T>G
NM_000545.8:c.737T>G
NM_000545.8(HNF1A):c.737T>G (p.Val246Gly)

Likely Pathogenic

Met criteria codes 5
PP4 PP3 PM5 PM2_Supporting PM1_Supporting
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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.737T>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of valine to glycine at codon 246 (p.(Val2466Gly)) 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). It 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). Another missense variant, c.736G>T (p.Val246Leu)​ has been interpreted as pathogenic by the ClinGen MDEP and has a greater Grantham distance (PM5). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). This variant was identified in two 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). One of these individuals has a MODY probability calculator result below 50% but has had persistent C-peptide for 27 years, and had negative genetic testing for HNF4A) (PP4; internal lab contributor). Taken together, this evidence supports the classification of this variant as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 6/4/2021): PM5, PP3, PP4, PM1_Supporting, PM2_Supporting.
Met criteria codes
PP4
This variant was identified in an individual with a MODY probability calculator result below 50% but has had persistent C-peptide for 27 years, and had 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).
PM5
Another missense variant, c.736G>T (p.Val246Leu)​ has been interpreted as pathogenic by the ClinGen MDEP and has a greater Grantham distance (PM5).
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
PS4
This variant was identified in two 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).
Approved on: 2021-12-28
Published on: 2022-07-11
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