6-28287103-CAT-TAC

Variant names:

• chr6-28287103-CAT-TAC
• NM_032507.4:c.577_579delCATinsTAC
• PGBD1 p.His193Tyr

Variant summary

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

The NM_032507.4(PGBD1):​c.577_579delCATinsTAC​(p.His193Tyr) variant causes a missense change involving the alteration of a non-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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H193R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PGBD1 NM_032507.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 0 publications found

Genes affected

PGBD1 (HGNC:19398): (piggyBac transposable element derived 1) The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived (PGBD) genes. The PGBD proteins appear to be novel, with no obvious relationship to other transposases, or other known protein families. This gene product is specifically expressed in the brain, however, its exact function is not known. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, May 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032507.4. 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
	PGBD1	NM_032507.4	MANE Select	c.577_579delCATinsTAC	p.His193Tyr	missense	N/A	NP_115896.1	Q96JS3
	PGBD1	NM_001184743.2		c.577_579delCATinsTAC	p.His193Tyr	missense	N/A	NP_001171672.1	Q96JS3
	PGBD1	NM_001386059.1		c.577_579delCATinsTAC	p.His193Tyr	missense	N/A	NP_001372988.1	Q96JS3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGBD1	ENST00000682144.1	MANE Select	c.577_579delCATinsTAC	p.His193Tyr	missense	N/A	ENSP00000506997.1	Q96JS3
	PGBD1	ENST00000259883.3	TSL:1	c.577_579delCATinsTAC	p.His193Tyr	missense	N/A	ENSP00000259883.3	Q96JS3
	PGBD1	ENST00000918204.1		c.577_579delCATinsTAC	p.His193Tyr	missense	N/A	ENSP00000588263.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.34

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: chr6-28254880;