22-29441580-CTC-GTG

Variant names:

• chr22-29441580-CTC-GTG
• NM_021026.2:c.412_414delCTCinsGTG
• RFPL1 p.Leu138Val

Variant summary

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

The NM_021026.2(RFPL1):​c.412_414delCTCinsGTG​(p.Leu138Val) variant causes a missense change. 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. L138F) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 0)
• Consequence: RFPL1 NM_021026.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.63
• Publications: 0 publications found

Genes affected

RFPL1 (HGNC:9977): (ret finger protein like 1) Predicted to enable ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of G2/M transition of mitotic cell cycle; negative regulation of cell division; and positive regulation of proteolysis. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

RFPL1S (HGNC:9978): (RFPL1 antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021026.2. 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
	RFPL1	NM_021026.2	MANE Select	c.412_414delCTCinsGTG	p.Leu138Val	missense	N/A	NP_066306.2	O75677
	RFPL1	NM_001393612.1		c.325_327delCTCinsGTG	p.Leu109Val	missense	N/A	NP_001380541.1
	RFPL1S	NR_002727.2		n.548_550delGAGinsCAC		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFPL1	ENST00000354373.2	TSL:1 MANE Select	c.412_414delCTCinsGTG	p.Leu138Val	missense	N/A	ENSP00000346342.2	O75677
	RFPL1S	ENST00000248980.9	TSL:1	n.272-2389_272-2387delGAGinsCAC		intron	N/A
	RFPL1S	ENST00000461286.4	TSL:4	n.855_857delGAGinsCAC		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.6

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: chr22-29837569;