3-73624277-CGC-AGT

Variant names:

• chr3-73624277-CGC-AGT
• NM_015009.3:c.547_549delGCGinsACT
• PDZRN3 p.Ala183Thr

Variant summary

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

The NM_015009.3(PDZRN3):​c.547_549delGCGinsACT​(p.Ala183Thr) 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. A183S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PDZRN3 NM_015009.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.46
• Publications: 0 publications found

Genes affected

PDZRN3 (HGNC:17704): (PDZ domain containing ring finger 3) This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted for degradation by the human papilloma virus E6 protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

PDZRN3-AS1 (HGNC:40814): (PDZRN3 antisense RNA 1)

ENSG00000278934 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015009.3. 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
	PDZRN3	NM_015009.3	MANE Select	c.547_549delGCGinsACT	p.Ala183Thr	missense	N/A	NP_055824.1	Q9UPQ7-1
	PDZRN3-AS1	NR_046681.1		n.398+312_398+314delCGCinsAGT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDZRN3	ENST00000263666.9	TSL:1 MANE Select	c.547_549delGCGinsACT	p.Ala183Thr	missense	N/A	ENSP00000263666.4	Q9UPQ7-1
	PDZRN3	ENST00000308537.4	TSL:1	c.547_549delGCGinsACT	p.Ala183Thr	missense	N/A	ENSP00000308831.4	Q9UPQ7-2
	PDZRN3-AS1	ENST00000478988.3	TSL:5	n.380+312_380+314delCGCinsAGT		intron	N/A

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		3.5

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: chr3-73673428;