12-120978486-A-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2PP5_Very_StrongBP4
The ENST00000433033.3(HNF1A-AS1):n.134+1128T>G variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★).
Frequency
Consequence
ENST00000433033.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF1A-AS1 | ENST00000433033.3 | n.134+1128T>G | intron_variant | Intron 1 of 3 | 3 | |||||
HNF1A-AS1 | ENST00000535301.2 | n.322+2158T>G | intron_variant | Intron 1 of 1 | 4 | |||||
HNF1A-AS1 | ENST00000537361.1 | n.263+2158T>G | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Published functional studies demonstrate this variant has significantly decreased luciferase activity compared to wild-type (Godart et al., 2000; Lausen et al., 2000; Radha et al., 2009); No data available from control populations to assess the frequency of this variant; This variant is associated with the following publications: (PMID: 19336507, 10606640, 22413961, 23348805, 11692182, 10649494, 9313764) -
This variant occurs in a non-coding region of the HNF1A gene. It does not change the encoded amino acid sequence of the HNF1A protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with maturity-onset diabetes of the young (PMID: 9313764). It has also been observed to segregate with disease in related individuals. This variant is also known as A>C substitution at nucleotide -58. Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects HNF1A function (PMID: 10649494). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Monogenic diabetes Pathogenic:1
The c.-283A>C in the HNF1 homeobox A gene, HNF1A, is a single nucleotide variant in the promoter of NM_000545.8. This variant is located within the HNF4A binding domain (c.-276 to c.-288) of HNF1A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting). Functional studies demonstrated the c.-283A>C protein has transactivation below 40% of wildtype, indicating that this variant impacts protein function (PS3_Supporting; PMID:10649494). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), however it was identified in at least one individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and sulfonylurea sensitive) (PP4_Moderate; internal lab contributor). This variant also segregated with diabetes, with 7 informative meioses in two families with MODY (PP1_Strong; PMID:9313764; internal lab contributor). Taken together, this evidence suggests the classification of this variant as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.0_: PP1_Strong, PP4_moderate, PM1_Supporting, PM2_Supporting, PS3_Supporting). -
Maturity-onset diabetes of the young type 3 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.