chr1-155610292-A-G

Variant names:

• chr1-155610292-A-G
• rs926774989
• NM_018116.4:c.44A>G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_018116.4(MSTO1):​c.44A>G​(p.His15Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000107 in 930,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 0.0000011 (0 hom.)
• Consequence: MSTO1 NM_018116.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.51

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]

ENSG00000232519 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.786

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSTO1	NM_018116.4	c.44A>G	p.His15Arg	missense_variant	Exon 1 of 14	ENST00000245564.8	NP_060586.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSTO1	ENST00000245564.8	c.44A>G	p.His15Arg	missense_variant	Exon 1 of 14	1	NM_018116.4	ENSP00000245564.3
MSTO1	ENST00000368341.8	c.44A>G	p.His15Arg	missense_variant	Exon 1 of 13	2		ENSP00000357325.4

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.00000107 AC: 1 AN: 930416 Hom.: 0 Cov.: 12 AF XY: 0.00000214 AC XY: 1 AN XY: 466774

Gnomad4 AFR exome AF: 0.0000462

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000416

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Apr 23, 2021

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MSTO1 c.44A>G (p.His15Arg) results in a non-conservative amino acid change located in the Misato Segment II tubulin-like domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 119222 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.44A>G in individuals affected with Mitochondrial Myopathy-Cerebellar Ataxia-Pigmentary Retinopathy Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.54
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Uncertain	25
DANN	Benign	0.94
DEOGEN2	Benign	0.060	.;T;.
Eigen	Benign	-0.12
Eigen_PC	Benign	-0.16
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.65	T;T;T
M_CAP	Benign	0.018	T
MetaRNN	Pathogenic	0.79	D;D;D
MetaSVM	Benign	-0.95	T
MutationAssessor	Uncertain	2.2	.;M;M
PrimateAI	Pathogenic	0.93	D
PROVEAN	Pathogenic	-4.8	.;D;D
REVEL	Uncertain	0.48
Sift	Uncertain	0.019	.;D;D
Sift4G	Uncertain	0.037	.;D;D
Polyphen		0.88	.;P;.
Vest4		0.66, 0.65
MutPred		0.76		Gain of MoRF binding (P = 0.0146);Gain of MoRF binding (P = 0.0146);Gain of MoRF binding (P = 0.0146);
MVP		0.69
MPC		3.9
ClinPred		0.92	D
GERP RS		3.3
Varity_R		0.35
gMVP		0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs926774989; hg19: chr1-155580083;