rs1554507029

Variant names:

• chr8-17723281-ATATTAGTCCTATTACACAAAATCTAGCATCCAAAGATTCCACAGGAGATAGTCTTTTGCAAAGTAAATGAAACTGAAATAATCTTTTTTTCTGATTCCAGTTAGAGTCCAAATCCCCTGGGTTGCTACTCTTAAACCTCCAAAACACCATCACTTCAGACGATGCACTTTCGAATCCTTCATGCAAAAATATACTTTAACACATAATTATTTCAAGAGTGTTTTTCAAAGAATTTTTTTTCTGCCAAACTTTCAGAGCAACTCCAAGGAAGCAGTATGCCTATTTTTCCTGAAACCCCAGAAACAAAAATTCTAATTATTTGCAGAGCATTAGTTTTTCTTGTAATGACTGTTTCCACAACCCCCGAAGTGTGATATAAAGTCGACTTACAATTGTTGCTGTAAGTGCTCAGCTCACTGTGGGTGCTGGCTATTGAGGGGGTGCTTCCTGTCCTCCGCAGCGCAGGACTTTTCAAAGATGCTTTGGATTTAGGAAGTGGTCTAGGCAAATTCACCCATGACGACTGTGCAGTTTTCAAGGATGTAGGCTTTCCTTGGGGTTTAAAAAAAACAAAAAGTTTCCAGTGCTATTCATCCCGAAAGCTGGCACTTTTTAAGCCTGTAAACTCAAACTTCTGCACTAACAACAAAGTCAAAACACAAAATGAATGTTCACAATCATGTAACTTCAGATGAAAGATGAAAGCTTCACGCAGACATGTTTATTTTTGATCATTTAGAGGCAAGAGAGCAGAAATGATGAGGCAATTAGGATATGAGAAGTGTAGGAGTAACCCTGTCTCCTAAAGTAATTAACTCACACATGTTCTCTGAAGGAGATGATCAATCAGAATAATCATGAGAAAGCAGCTTTTGGCAAAACTGAAATAAAAAAATAAACAAATTGATAC-A
• rs1554507029
• NM_001363059.2:c.2288-358_2449+390del

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PVS1_Moderate

The NM_001363059.2(MTUS1):​c.2288-358_2449+390del variant causes a exon loss, splice acceptor, splice donor, splice region, intron change involving the alteration of a non-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 DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MTUS1 NM_001363059.2 exon_loss, splice_acceptor, splice_donor, splice_region, intron
• Clinical Significance: not provided no classification provided O:2
• Conservation: PhyloP100: 1.54
• Publications: 0 publications found

Genes affected

MTUS1 (HGNC:29789): (microtubule associated scaffold protein 1) This gene encodes a protein which contains a C-terminal domain able to interact with the angiotension II (AT2) receptor and a large coiled-coil region allowing dimerization. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. One of the transcript variants has been shown to encode a mitochondrial protein that acts as a tumor suppressor and partcipates in AT2 signaling pathways. Other variants may encode nuclear or transmembrane proteins but it has not been determined whether they also participate in AT2 signaling pathways. [provided by RefSeq, Jul 2008]

ENSG00000301996 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.04248623 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363059.2. 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
	MTUS1	NM_001363059.2	MANE Select	c.2288-358_2449+390del		exon_loss splice_acceptor splice_donor splice_region intron	Exon 4 of 15	NP_001349988.1	Q9ULD2-1
	MTUS1	NM_001363057.2		c.2288-358_2449+390del		exon_loss splice_acceptor splice_donor splice_region intron	Exon 4 of 15	NP_001349986.1
	MTUS1	NM_001001924.3		c.2288-358_2449+390del		exon_loss splice_acceptor splice_donor splice_region intron	Exon 4 of 15	NP_001001924.1	Q9ULD2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTUS1	ENST00000693296.1	MANE Select	c.2288-358_2449+390del		exon_loss splice_acceptor splice_donor splice_region intron	Exon 4 of 15	ENSP00000509719.1	Q9ULD2-1
	MTUS1	ENST00000262102.10	TSL:1	c.2288-358_2449+390del		exon_loss splice_acceptor splice_donor splice_region intron	Exon 4 of 15	ENSP00000262102.6	Q9ULD2-1
	MTUS1	ENST00000520196.5	TSL:1	n.1490-29_*197+390del		exon_loss	Exon 3 of 15	ENSP00000431016.1	H0YC63

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	Gestational diabetes mellitus uncontrolled (1)
-	-	-	Normal pregnancy (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1554507029; hg19: chr8-17580790;