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.794A>G (p.Tyr265Cys)

CA386966196

1338571 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: b9f03f45-e3ce-41d6-944e-5a63ad5d4b9b

HGVS expressions

NM_000545.8:c.794A>G
NM_000545.8(HNF1A):c.794A>G (p.Tyr265Cys)
NC_000012.12:g.120994244A>G
CM000674.2:g.120994244A>G
NC_000012.11:g.121432047A>G
CM000674.1:g.121432047A>G
NC_000012.10:g.119916430A>G
NG_011731.2:g.20499A>G
ENST00000257555.11:c.794A>G
ENST00000257555.10:c.794A>G
ENST00000400024.6:c.794A>G
ENST00000402929.5:n.929A>G
ENST00000535955.5:n.43-3247A>G
ENST00000538626.2:n.191-3247A>G
ENST00000538646.5:c.607A>G
ENST00000540108.1:c.*234A>G
ENST00000541395.5:c.794A>G
ENST00000541924.5:c.713+538A>G
ENST00000543427.5:c.633+618A>G
ENST00000544413.2:c.794A>G
ENST00000544574.5:c.73-2373A>G
ENST00000560968.5:n.893+44A>G
ENST00000615446.4:c.-257-2018A>G
ENST00000617366.4:c.586+665A>G
NM_000545.5:c.794A>G
NM_000545.6:c.794A>G
NM_001306179.1:c.794A>G
NM_001306179.2:c.794A>G

Uncertain Significance

Met criteria codes 3
PP3 PM1 PM2_Supporting
Not Met criteria codes 2
PS4 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.794A>G variant in the HNF1 homeobox A gene, HNF1A, causes an amino acid change of tyrosine to cysteine at codon 265 (p.Tyr265Cys) 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 also is predicted to be deleterious by computational evidence, with a REVEL score of 0.941, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from 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 (PMID: 30663027, internal lab contributors). Another missense variant, c.794A>C (p.Tyr265Ser), has been classified as a VUS by the ClinGen MDEP; therefore, PM5 will not be applied. In summary, c.794A>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): PM1, PP3, PM2_Supporting.
Met criteria codes
PP3
REVEL = 0.941
PM1
Residue within the DNA binding domain that directly binds DNA.
PM2_Supporting
Absent in gnomAD.
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 (PMID: 30663027, internal lab contributors).
PM5
Another missense variant, c.794A>C (p.Tyr265Ser), has been classified as a VUS by the ClinGen MDEP; therefore, PM5 will not be applied.
Approved on: 2022-05-03
Published on: 2022-05-03
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.