PCYT2 p.Pro186Pro

Variant names:

• chr17-81906877-A-A
• NM_002861.5:c.

Your query was ambiguous. Multiple possible variants found:

• chr17-81906878--
• chr17-81906878-G-A
• chr17-81906878-G-T
• chr17-81906878-G-C

Variant summary

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

The NM_002861.5(PCYT2):​c. variant causes a exon region 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: 33)
• Consequence: PCYT2 NM_002861.5 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 0 publications found

Genes affected

PCYT2 (HGNC:8756): (phosphate cytidylyltransferase 2, ethanolamine) This gene encodes an enzyme that catalyzes the formation of CDP-ethanolamine from CTP and phosphoethanolamine in the Kennedy pathway of phospholipid synthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

PCYT2 Gene-Disease associations (from GenCC):

• spastic paraplegia 82, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

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_002861.5. 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
	PCYT2	NM_002861.5	MANE Select	c.		exon_region	Exon 7 of 13	NP_002852.1	Q99447-1
	PCYT2	NM_001184917.3		c.		exon_region	Exon 8 of 14	NP_001171846.1	Q99447-3
	PCYT2	NM_001330518.2		c.		exon_region	Exon 7 of 12	NP_001317447.1	I3L1R7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYT2	ENST00000538936.7	TSL:1 MANE Select	c.		exon_region	Exon 7 of 13	ENSP00000439245.3	Q99447-1
	PCYT2	ENST00000538721.6	TSL:1	c.		exon_region	Exon 8 of 14	ENSP00000442050.2	Q99447-3
	PCYT2	ENST00000883690.1		c.		exon_region	Exon 9 of 15	ENSP00000553749.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.55

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: chr17-79864753;