NM_006734.4:c.5614dupG

Variant names:

• chr6-142761469-T-TC
• rs869312844
• NM_006734.4:c.5614dupG

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_006734.4(HIVEP2):​c.5614dupG​(p.Glu1872GlyfsTer16) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HIVEP2 NM_006734.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.57
• Publications: 1 publications found

Genes affected

HIVEP2 (HGNC:4921): (HIVEP zinc finger 2) This gene encodes a member of a family of closely related, large, zinc finger-containing transcription factors. The encoded protein regulates transcription by binding to regulatory regions of various cellular and viral genes that maybe involved in growth, development and metastasis. The protein contains the ZAS domain comprised of two widely separated regions of zinc finger motifs, a stretch of highly acidic amino acids and a serine/threonine-rich sequence. [provided by RefSeq, Nov 2012]

HIVEP2 Gene-Disease associations (from GenCC):

• intellectual disability, autosomal dominant 43

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Illumina, G2P
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 6-142761469-T-TC is Pathogenic according to our data. Variant chr6-142761469-T-TC is described in ClinVar as Pathogenic. ClinVar VariationId is 224795.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006734.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP2	NM_006734.4	MANE Select	c.5614dupG	p.Glu1872GlyfsTer16	frameshift	Exon 8 of 10	NP_006725.3
	HIVEP2	NM_001438449.1		c.5614dupG	p.Glu1872GlyfsTer16	frameshift	Exon 8 of 10	NP_001425378.1
	HIVEP2	NM_001438450.1		c.5614dupG	p.Glu1872GlyfsTer16	frameshift	Exon 9 of 11	NP_001425379.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HIVEP2	ENST00000367603.8	TSL:1 MANE Select	c.5614dupG	p.Glu1872GlyfsTer16	frameshift	Exon 8 of 10	ENSP00000356575.2
	HIVEP2	ENST00000012134.7	TSL:5	c.5614dupG	p.Glu1872GlyfsTer16	frameshift	Exon 7 of 9	ENSP00000012134.2
	HIVEP2	ENST00000367604.6	TSL:5	c.5614dupG	p.Glu1872GlyfsTer16	frameshift	Exon 8 of 10	ENSP00000356576.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 25

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual disability, autosomal dominant 43 Pathogenic:1

Apr 20, 2022

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

not provided Pathogenic:1

Mar 17, 2016

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.5614dupG variant in the HIVEP2 gene has been observed in internal GeneDx whole exome sequencing data in association with developmental delay, hypertonia and spasticity. The c.5614dupG variant causes a frameshift starting with codon Glutamic Acid 1872, changes this amino acid to a Glycine residue, and creates a premature Stop codon at position 16 of the new reading frame, denoted p.Glu1872GlyfsX16. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.5614dupG variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.5614dupG as a pathogenic variant.

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.6
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs869312844; hg19: chr6-143082606;