PLPP6 p.Ser63Ser

Variant names:

• chr9-4662561-G-G
• NM_001353486.2:c.

Your query was ambiguous. Multiple possible variants found:

• chr9-4662562--
• chr9-4662564-C-T
• chr9-4662562-AG-TC
• chr9-4662562-AGC-TCT
• chr9-4662562-AGC-TCA
• chr9-4662562-AGC-TCG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001353486.2(SPATA6L):​c. variant causes a intron 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: 32)
• Consequence: SPATA6L NM_001353486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89
• Publications: 0 publications found

Genes affected

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]

PLPP6 (HGNC:23682): (phospholipid phosphatase 6) Enables lipid phosphatase activity. Involved in phospholipid dephosphorylation. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353486.2. 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
	SPATA6L	NM_001353486.2	MANE Select	c.		intron	N/A	NP_001340415.1	Q8N4H0-1
	SPATA6L	NM_001353484.2		c.		intron	N/A	NP_001340413.1	A0AA34QVF8
	SPATA6L	NM_001353485.2		c.		intron	N/A	NP_001340414.1	A0AA34QVF8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA6L	ENST00000682582.1	MANE Select	c.		intron	N/A	ENSP00000506787.1	Q8N4H0-1
	SPATA6L	ENST00000451763.6	TSL:1	n.		intron	N/A
	SPATA6L	ENST00000707146.1		c.		intron	N/A	ENSP00000516765.1	A0AA34QVF8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

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: chr9-4662561;