NM_001077663.3:c.2092_2094delGTCinsATA

Variant names:

• chr7-43877369-GAC-TAT
• NM_001077663.3:c.2092_2094delGTCinsATA
• URGCP p.Val698Ile

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001077663.3(URGCP):​c.2092_2094delGTCinsATA​(p.Val698Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: URGCP NM_001077663.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.16
• Publications: 0 publications found

Genes affected

URGCP (HGNC:30890): (upregulator of cell proliferation) URG4 is upregulated in the presence of hepatitis B virus (HBV)-encoded X antigen (HBxAg) and may contribute to the development of hepatocellular carcinoma by promoting hepatocellular growth and survival (Tufan et al., 2002 [PubMed 12082552]).[supplied by OMIM, Mar 2008]

URGCP-MRPS24 (HGNC:49188): (URGCP-MRPS24 readthrough) This locus represents naturally occurring read-through transcription between the neighboring URGCP (upregulator of cell proliferation) and MRPS24 (mitochondrial ribosomal protein S24) genes on chromosome 7. The read-through transcript is predicted to encode a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to a frameshift relative to the downstream gene. [provided by RefSeq, Mar 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077663.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URGCP	NM_001077663.3	MANE Select	c.2092_2094delGTCinsATA	p.Val698Ile	missense	N/A	NP_001071131.1	Q8TCY9-1
	URGCP	NM_017920.5		c.2065_2067delGTCinsATA	p.Val689Ile	missense	N/A	NP_060390.3
	URGCP	NM_001077664.3		c.1963_1965delGTCinsATA	p.Val655Ile	missense	N/A	NP_001071132.1	Q8TCY9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URGCP	ENST00000453200.6	TSL:1 MANE Select	c.2092_2094delGTCinsATA	p.Val698Ile	missense	N/A	ENSP00000396918.1	Q8TCY9-1
	URGCP	ENST00000402306.7	TSL:1	c.2065_2067delGTCinsATA	p.Val689Ile	missense	N/A	ENSP00000384955.3	Q8TCY9-2
	URGCP	ENST00000336086.10	TSL:1	c.1963_1965delGTCinsATA	p.Val655Ile	missense	N/A	ENSP00000336872.6	Q8TCY9-4

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-43916968;