1-155610494-C-G

Variant names:

• chr1-155610494-C-G
• NM_018116.4:c.154C>G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP3_Strong

The NM_001350776.1(MSTO1):​c.-134C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 16)
• Consequence: MSTO1 NM_001350776.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.47

Genes affected

MSTO1 (HGNC:29678): (misato mitochondrial distribution and morphology regulator 1) Involved in mitochondrion distribution. Located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105371452 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.978

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSTO1	NM_018116.4	c.154C>G	p.Arg52Gly	missense_variant	Exon 2 of 14	ENST00000245564.8	NP_060586.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSTO1	ENST00000245564.8	c.154C>G	p.Arg52Gly	missense_variant	Exon 2 of 14	1	NM_018116.4	ENSP00000245564.3
MSTO1	ENST00000368341.8	c.154C>G	p.Arg52Gly	missense_variant	Exon 2 of 13	2		ENSP00000357325.4

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 16

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome Uncertain:1

-

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting+PM1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.88
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.33	.;T;.
Eigen	Benign	0.17
Eigen_PC	Benign	-0.057
FATHMM_MKL	Benign	0.69	D
LIST_S2	Uncertain	0.90	D;D;T
M_CAP	Benign	0.038	D
MetaRNN	Pathogenic	0.98	D;D;D
MetaSVM	Uncertain	-0.22	T
MutationAssessor	Pathogenic	3.3	.;M;M
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-6.0	.;D;D
REVEL	Uncertain	0.56
Sift	Uncertain	0.0030	.;D;D
Sift4G	Uncertain	0.0050	.;D;D
Polyphen		1.0	.;D;.
Vest4		0.82, 0.77
MutPred		0.95		Loss of catalytic residue at R52 (P = 0.0636);Loss of catalytic residue at R52 (P = 0.0636);Loss of catalytic residue at R52 (P = 0.0636);
MVP		0.76
MPC		4.2
ClinPred		0.99	D
GERP RS		2.3
Varity_R		0.60
gMVP		0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-155580285;