chr20-44355804-CA-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPP4_ModeratePP1PM2_Supporting
This summary comes from the ClinGen Evidence Repository: The c.1del variant in the hepatic nuclear factor 4-alpha gene, HNF4A, results in the loss of the initiation codon (p.Met1?) of NM_175914.5. By altering the start codon of the coding sequence, this variant may cause a truncated or absent protein in a gene in which loss-of-function is an established disease mechanism (PMID:23348805).This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sulfonylurea responsive) (PP4_Moderate; Internal lab contributor). This variant segregated with diabetes, with three informative meioses in one family (PP1; Internal lab contributors). In summary, c.1del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 10/11/1024): PVS1_Strong, PP4_Moderate, PP1, PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA2499225757/MONDO:0015967/085
Frequency
Consequence
NM_175914.5 frameshift, start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNF4A | NM_175914.5 | c.1del | p.Met1? | frameshift_variant, start_lost | 1/10 | ENST00000316673.9 | NP_787110.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF4A | ENST00000316673.9 | c.1del | p.Met1? | frameshift_variant, start_lost | 1/10 | 1 | NM_175914.5 | ENSP00000315180 | ||
HNF4A | ENST00000457232.5 | c.1del | p.Met1? | frameshift_variant, start_lost | 1/10 | 1 | ENSP00000396216 | |||
HNF4A | ENST00000609795.5 | c.1del | p.Met1? | frameshift_variant, start_lost | 1/8 | 1 | ENSP00000476609 | |||
HNF4A | ENST00000609262.5 | c.-231del | 5_prime_UTR_variant | 1/4 | 1 | ENSP00000476310 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Monogenic diabetes Pathogenic:1
Likely pathogenic, reviewed by expert panel | curation | ClinGen Monogenic Diabetes Variant Curation Expert Panel | Apr 06, 2024 | The c.1del variant in the hepatic nuclear factor 4-alpha gene, HNF4A, results in the loss of the initiation codon (p.Met1?) of NM_175914.5. By altering the start codon of the coding sequence, this variant may cause a truncated or absent protein in a gene in which loss-of-function is an established disease mechanism (PMID: 23348805).This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sulfonylurea responsive) (PP4_Moderate; Internal lab contributor). This variant segregated with diabetes, with three informative meioses in one family (PP1; Internal lab contributors). In summary, c.1del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 2.0.0, approved 10/11/1024): PVS1_Strong, PP4_Moderate, PP1, PM2_Supporting. - |
Maturity-onset diabetes of the young type 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Exeter Molecular Genetics Laboratory | Oct 05, 2021 | The c.1del variant in the HNF4 homeobox A gene, HNF4A, results in the loss of the initiation codon (p.Met1?) in exon 1 of the pancreatic specific HNF4A isoform NM_175914.5. By altering the start codon of the coding sequence, this variant may cause a truncated or absent protein in a gene in which loss-of-function is an established disease mechanism (PVS1_Moderate; PMID: 23348805). This variant is absent in gnomAD v2.1.1 (PM2_Supporting), and was identified in one individual in our laboratory 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. This individual has a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and sensitive so sulfonylureas) (PP4_Moderate). This variant segregated with diabetes, with three informative meioses in this individual's family (PP1_Supporting). In summary, c.1del meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied: PVS1_Moderate, PP4_Moderate, PP1_Supporting, PM2_Supporting. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.