3-146455305-TC-CT

Variant names:

• chr3-146455305-TC-CT
• NM_001395437.1:c.254_255delGAinsAG
• PLSCR2 p.Arg85Gln

Variant summary

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

The NM_001395437.1(PLSCR2):​c.254_255delGAinsAG​(p.Arg85Gln) 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 Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLSCR2 NM_001395437.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 0 publications found

Genes affected

PLSCR2 (HGNC:16494): (phospholipid scramblase 2) This gene encodes a member of the phospholipid scramblase family. Phospholipid scramblases are membrane proteins that mediate calcium-dependent, non-specific movement of plasma membrane phospholipids and phosphatidylserine exposure. The encoded protein contains a low affinity calcium binding motif and may play a role in blood coagulation and apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395437.1. 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
	PLSCR2	NM_001395437.1	MANE Select	c.254_255delGAinsAG	p.Arg85Gln	missense	N/A	NP_001382366.1	Q9NRY7-1
	PLSCR2	NM_001199978.3		c.473_474delGAinsAG	p.Arg158Gln	missense	N/A	NP_001186907.1	Q9NRY7-2
	PLSCR2	NM_001395440.1		c.473_474delGAinsAG	p.Arg158Gln	missense	N/A	NP_001382369.1	Q9NRY7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLSCR2	ENST00000696113.1	MANE Select	c.254_255delGAinsAG	p.Arg85Gln	missense	N/A	ENSP00000512407.1	Q9NRY7-1
	PLSCR2	ENST00000613069.4	TSL:1	c.461_462delGAinsAG	p.Arg154Gln	missense	N/A	ENSP00000478902.1	Q9NRY7-3
	PLSCR2	ENST00000336685.6	TSL:1	c.254_255delGAinsAG	p.Arg85Gln	missense	N/A	ENSP00000338707.2	Q9NRY7-1

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		-0.21

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: chr3-146173092;