X-49178431-G-A

Variant names:

• chrX-49178431-G-A
• rs1057519388
• NM_006150.5:c.609C>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP7

The NM_006150.5(PRICKLE3):​c.609C>T​(p.Ser203Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 24)
• Consequence: PRICKLE3 NM_006150.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 0 publications found

Genes affected

PRICKLE3 (HGNC:6645): (prickle planar cell polarity protein 3) LIM domain only 6 is a three LIM domain-containing protein. The LIM domain is a cysteine-rich sequence motif that binds zinc atoms to form a specific protein-binding interface for protein-protein interactions. [provided by RefSeq, Jul 2008]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP7: Synonymous conserved (PhyloP=0.039 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006150.5. 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
	PRICKLE3	NM_006150.5	MANE Select	c.609C>T	p.Ser203Ser	synonymous	Exon 6 of 9	NP_006141.2
	PRICKLE3	NM_001307979.2		c.405C>T	p.Ser135Ser	synonymous	Exon 6 of 9	NP_001294908.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRICKLE3	ENST00000599218.6	TSL:1 MANE Select	c.609C>T	p.Ser203Ser	synonymous	Exon 6 of 9	ENSP00000470248.1
	PRICKLE3	ENST00000453382.5	TSL:5	c.405C>T	p.Ser135Ser	synonymous	Exon 5 of 8	ENSP00000388599.2
	PRICKLE3	ENST00000432913.5	TSL:5	c.405C>T	p.Ser135Ser	synonymous	Exon 6 of 7	ENSP00000390620.2

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.5
DANN	Benign	0.82
PhyloP100		0.039
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1057519388; hg19: chrX-49034780;