chr10-3101506-CTC-TTG

Variant names:

• chr10-3101506-CTC-TTG
• NM_002627.5:c.406_408delCTCinsTTG
• PFKP p.137

Variant summary

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

The NM_002627.5(PFKP):​c.406_408delCTCinsTTG​(p.137) variant causes a synonymous change. 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. Synonymous variant affecting the same amino acid position (i.e. L136L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: PFKP NM_002627.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.01
• Publications: 0 publications found

Genes affected

PFKP (HGNC:8878): (phosphofructokinase, platelet) This gene encodes a member of the phosphofructokinase A protein family. The encoded enzyme is the platelet-specific isoform of phosphofructokinase and plays a key role in glycolysis regulation. This gene may play a role in metabolic reprogramming in some cancers, including clear cell renal cell carcinomas, and cancer of the bladder, breast, and lung. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002627.5. 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
	PFKP	NM_002627.5	MANE Select	c.406_408delCTCinsTTG	p.137	synonymous	N/A	NP_002618.1	Q01813-1
	PFKP	NM_001410880.1		c.406_408delCTCinsTTG	p.137	synonymous	N/A	NP_001397809.1	A0A8V8TMY4
	PFKP	NM_001242339.2		c.382_384delCTCinsTTG	p.129	synonymous	N/A	NP_001229268.1	Q01813-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PFKP	ENST00000381125.9	TSL:1 MANE Select	c.406_408delCTCinsTTG	p.137	synonymous	N/A	ENSP00000370517.4	Q01813-1
	PFKP	ENST00000867381.1		c.422_424delCTCinsTTG	p.ProLeu141LeuVal	missense	N/A	ENSP00000537440.1
	PFKP	ENST00000699222.1		c.406_408delCTCinsTTG	p.137	synonymous	N/A	ENSP00000514216.1	A0A8V8TMY4

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.0

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: chr10-3143698;