GeneBe

11-118407033-T-G

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_006476.5(ATP5MG):​c.149T>G​(p.Ile50Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. I50T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

ATP5MG
NM_006476.5 missense

Scores

3
5
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.50

Publications

0 publications found
Variant links:
Genes affected
ATP5MG (HGNC:14247): (ATP synthase membrane subunit g) Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The Fo seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the g subunit of the Fo complex. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.36289546).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006476.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ATP5MG
NM_006476.5
MANE Select
c.149T>Gp.Ile50Ser
missense
Exon 2 of 3NP_006467.4
ATP5MG
NR_033759.2
n.262T>G
non_coding_transcript_exon
Exon 3 of 4
LOC100131626
NR_046369.1
n.231+10308A>C
intron
N/A

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ATP5MG
ENST00000300688.8
TSL:1 MANE Select
c.149T>Gp.Ile50Ser
missense
Exon 2 of 3ENSP00000300688.3O75964
ENSG00000285827
ENST00000648261.1
c.-799+5316T>G
intron
N/AENSP00000498126.1A0A3B3ITZ1
ATP5MG
ENST00000856737.1
c.296T>Gp.Ile99Ser
missense
Exon 2 of 3ENSP00000526796.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.040
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.090
T
Eigen
Benign
0.15
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.73
T
M_CAP
Benign
0.0038
T
MetaRNN
Benign
0.36
T
MetaSVM
Benign
-0.65
T
MutationAssessor
Benign
1.8
L
PhyloP100
7.5
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-0.86
N
REVEL
Uncertain
0.30
Sift
Benign
0.66
T
Sift4G
Benign
0.72
T
Polyphen
0.013
B
Vest4
0.84
MutPred
0.50
Gain of disorder (P = 0.0017)
MVP
0.44
MPC
0.20
ClinPred
0.69
D
GERP RS
6.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.18
gMVP
0.95
Mutation Taster
=47/53
disease causing

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs11549141; hg19: chr11-118277748; API