6-152990006-ATG-TAA

Variant names:

• chr6-152990006-ATG-TAA
• NM_019041.7:c.1030_1032delCATinsTTA
• MTRF1L p.His344Leu

Variant summary

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

The NM_019041.7(MTRF1L):​c.1030_1032delCATinsTTA​(p.His344Leu) variant causes a missense change involving the alteration of a conserved nucleotide. 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: MTRF1L NM_019041.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.46
• Publications: 0 publications found

Genes affected

MTRF1L (HGNC:21051): (mitochondrial translation release factor 1 like) The protein encoded by this gene plays a role in mitochondrial translation termination, and is thought to be a release factor that is involved in the dissociation of the complete protein from the final tRNA, the ribosome, and the cognate mRNA. This protein acts upon UAA and UAG stop codons, but has no in vitro activity against UGA, which encodes tryptophan in human mitochondrion, or, the mitochondrial non-cognate stop codons, AGA and AGG. This protein shares sequence similarity to bacterial release factors. Pseudogenes of this gene are found on chromosomes 4, 8, and 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2014]

ENSG00000227627 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019041.7. 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
	MTRF1L	NM_019041.7	MANE Select	c.1030_1032delCATinsTTA	p.His344Leu	missense	N/A	NP_061914.3
	MTRF1L	NM_001301870.2		c.922_924delCATinsTTA	p.His308Leu	missense	N/A	NP_001288799.1
	MTRF1L	NM_001301871.2		c.604_606delCATinsTTA	p.His202Leu	missense	N/A	NP_001288800.1	Q9UGC7-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTRF1L	ENST00000367233.10	TSL:1 MANE Select	c.1030_1032delCATinsTTA	p.His344Leu	missense	N/A	ENSP00000356202.5	Q9UGC7-1
	MTRF1L	ENST00000367231.9	TSL:1	c.*77_*79delCATinsTTA		3_prime_UTR	Exon 6 of 6	ENSP00000356200.5	Q9UGC7-2
	MTRF1L	ENST00000367230.5	TSL:1	c.*77_*79delCATinsTTA		3_prime_UTR	Exon 6 of 6	ENSP00000356199.1	Q9UGC7-4

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.5

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: chr6-153311141;