20-44355850-T-TA

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_175914.5(HNF4A):c.47dup(p.Tyr16Ter) variant causes a stop gained, frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: HNF4A NM_175914.5 stop_gained, frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 5.46

Genes affected

HNF4A (HGNC:5024): (hepatocyte nuclear factor 4 alpha) The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants encoding several different isoforms. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 174 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 20-44355850-T-TA is Pathogenic according to our data. Variant chr20-44355850-T-TA is described in ClinVar as [Pathogenic]. Clinvar id is 1691373.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HNF4A	NM_175914.5	c.47dup	p.Tyr16Ter	stop_gained, frameshift_variant	1/10	ENST00000316673.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNF4A	ENST00000316673.9	c.47dup	p.Tyr16Ter	stop_gained, frameshift_variant	1/10	1	NM_175914.5
HNF4A	ENST00000457232.5	c.47dup	p.Tyr16Ter	stop_gained, frameshift_variant	1/10	1
HNF4A	ENST00000609795.5	c.47dup	p.Tyr16Ter	stop_gained, frameshift_variant	1/8	1
HNF4A	ENST00000609262.5	c.-185dup		5_prime_UTR_variant	1/4	1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hyperinsulinism due to HNF1A deficiency Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital

Dec 13, 2019

The duplication of a single nucleotide in the first exon of HNF4A introduces a premature stop codon (p.Tyr16*). This variant is predicted to result in a loss of gene function. This is a novel duplication that has not been reported in the medical literature or in clinical databases. This variant has not been observed in presumably healthy controls in the Genome Aggregation Database. While this variant appears to be novel, a different sequence change that also results in p.Tyr16* (c.48C>G), as well as other nonsense variants in HNF4A, have been described in several individuals with congenital hyperinsulinism (PMID: 20164212, PMID: 17407387, PMID: 23348805 and others). -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-42984490;