Genetic Variant MSTO1:p.Ser38Phe (chr1-155610453-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_018116.4(MSTO1):c.113C>T(p.Ser38Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S38C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 19)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MSTO1
NM_018116.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.414

Publications

0 publications found

Variant links:

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]

MSTO1 Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Broad Center for Mendelian Genomics, Ambry Genetics

MSTO1 links:

LOC105371452 (HGNC:):

LOC105371452 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.10719156).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018116.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MSTO1	NM_018116.4	MANE Select	c.113C>T	p.Ser38Phe	missense	Exon 2 of 14	NP_060586.2
MSTO1	NM_001256532.1		c.113C>T	p.Ser38Phe	missense	Exon 2 of 14	NP_001243461.1	Q9BUK6-2
MSTO1	NM_001350772.1		c.113C>T	p.Ser38Phe	missense	Exon 2 of 14	NP_001337701.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MSTO1	ENST00000245564.8	TSL:1 MANE Select	c.113C>T	p.Ser38Phe	missense	Exon 2 of 14	ENSP00000245564.3	Q9BUK6-1
MSTO1	ENST00000368341.8	TSL:2	c.113C>T	p.Ser38Phe	missense	Exon 2 of 13	ENSP00000357325.4	Q9BUK6-7
MSTO1	ENST00000490743.5	TSL:1	n.113C>T		non_coding_transcript_exon	Exon 2 of 13	ENSP00000476353.1	Q9BUK6-4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

698302

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

361112

African (AFR)

AF:

0.00

AC:

AN:

18400

American (AMR)

AF:

0.00

AC:

AN:

32290

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17920

East Asian (EAS)

AF:

0.00

AC:

AN:

32686

South Asian (SAS)

AF:

0.00

AC:

AN:

59328

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31882

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2576

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

468240

Other (OTH)

AF:

0.00

AC:

AN:

34980

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.050

Eigen

Benign

-0.80

Eigen_PC

Benign

-0.99

FATHMM_MKL

Benign

0.033

LIST_S2

Benign

0.58

M_CAP

Benign

0.012

MetaRNN

Benign

0.11

MetaSVM

Benign

-0.93

MutationAssessor

Benign

1.1

PhyloP100

0.41

PrimateAI

Uncertain

0.58

PROVEAN

Uncertain

-2.5

REVEL

Benign

0.094

Sift

Uncertain

0.019

Sift4G

Uncertain

0.050

Polyphen

0.58

Vest4

0.072

MutPred

0.36

Loss of disorder (P = 0.0216)

MVP

0.42

MPC

2.2

ClinPred

0.25

GERP RS

-1.8

PromoterAI

0.0056

Neutral

(source)

Varity_R

0.043

gMVP

0.31

Mutation Taster

=95/5

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over