METTL13 p.Tyr569Tyr

Variant names:

• chr1-171794406-C-C
• NM_015935.5:c.

Your query was ambiguous. Multiple possible variants found:

• chr1-171794407--
• chr1-171794409-C-T

Variant summary

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

The NM_015935.5(METTL13):​c. variant causes a exon region change involving the alteration of a 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: METTL13 NM_015935.5 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.39
• Publications: 0 publications found

Genes affected

METTL13 (HGNC:24248): (methyltransferase 13, eEF1A N-terminus and K55) Predicted to enable methyltransferase activity. Involved in negative regulation of cell cycle G1/S phase transition and negative regulation of transcription by RNA polymerase II. Predicted to be located in mitochondrion and nucleus. [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_015935.5. 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
	METTL13	NM_015935.5	MANE Select	c.		exon_region	Exon 6 of 8	NP_057019.3
	METTL13	NM_014955.3		c.		exon_region	Exon 6 of 8	NP_055770.1	Q8N6R0-3
	METTL13	NM_001007239.2		c.		exon_region	Exon 6 of 8	NP_001007240.1	Q8N6R0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	METTL13	ENST00000361735.4	TSL:1 MANE Select	c.		splice_donor intron	N/A	ENSP00000354920.3	Q8N6R0-5
	METTL13	ENST00000367737.9	TSL:1	c.		splice_donor intron	N/A	ENSP00000356711.5	Q8N6R0-1
	METTL13	ENST00000862970.1		c.		splice_donor intron	N/A	ENSP00000533029.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.4

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: chr1-171763546;