9-125747625-GAC-CAT

Variant names:

• chr9-125747625-GAC-CAT
• NM_006195.6:c.172_174delGACinsCAT
• PBX3 p.Asp58His

Variant summary

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

The NM_006195.6(PBX3):​c.172_174delGACinsCAT​(p.Asp58His) variant causes a missense change. 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: 29)
• Consequence: PBX3 NM_006195.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.99
• Publications: 0 publications found

Genes affected

PBX3 (HGNC:8634): (PBX homeobox 3) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in animal organ development; neuron development; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including adult locomotory behavior; dorsal spinal cord development; and regulation of respiratory gaseous exchange by nervous system process. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006195.6. 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
	PBX3	NM_006195.6	MANE Select	c.172_174delGACinsCAT	p.Asp58His	missense	N/A	NP_006186.1	P40426-1
	PBX3	NM_001411009.1		c.172_174delGACinsCAT	p.Asp58His	missense	N/A	NP_001397938.1	Q5JS98
	PBX3	NM_001330782.2		c.172_174delGACinsCAT	p.Asp58His	missense	N/A	NP_001317711.1	P40426-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBX3	ENST00000373489.10	TSL:1 MANE Select	c.172_174delGACinsCAT	p.Asp58His	missense	N/A	ENSP00000362588.5	P40426-1
	PBX3	ENST00000373482.6	TSL:1	n.172_174delGACinsCAT		non_coding_transcript_exon	Exon 1 of 8	ENSP00000362581.2	H3BLX0
	PBX3	ENST00000373492.6	TSL:1	n.172_174delGACinsCAT		non_coding_transcript_exon	Exon 1 of 7	ENSP00000362591.2	H3BLX0

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.0

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: chr9-128509904;