7-15686056-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005924.5(MEOX2):​c.347G>T​(p.Gly116Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,458 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G116E) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

MEOX2
NM_005924.5 missense

Scores

1
11
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.24
Variant links:
Genes affected
MEOX2 (HGNC:7014): (mesenchyme homeobox 2) This gene encodes a member of a subfamily of non-clustered, diverged, antennapedia-like homeobox-containing genes. The encoded protein may play a role in the regulation of vertebrate limb myogenesis. Mutations in the related mouse protein may be associated with craniofacial and/or skeletal abnormalities, in addition to neurovascular dysfunction observed in Alzheimer's disease. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MEOX2NM_005924.5 linkc.347G>T p.Gly116Val missense_variant Exon 1 of 3 ENST00000262041.6 NP_005915.2 P50222

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MEOX2ENST00000262041.6 linkc.347G>T p.Gly116Val missense_variant Exon 1 of 3 1 NM_005924.5 ENSP00000262041.5 P50222

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000443
AC:
1
AN:
225790
Hom.:
0
AF XY:
0.00000808
AC XY:
1
AN XY:
123696
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000991
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.90e-7
AC:
1
AN:
1449458
Hom.:
0
Cov.:
31
AF XY:
0.00000139
AC XY:
1
AN XY:
720916
show subpopulations
Gnomad4 AFR exome
AF:
0.00
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:
9.02e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.073
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.070
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.12
T
Eigen
Benign
0.11
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.73
T
M_CAP
Uncertain
0.27
D
MetaRNN
Uncertain
0.44
T
MetaSVM
Uncertain
-0.15
T
MutationAssessor
Benign
1.8
L
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-1.7
N
REVEL
Uncertain
0.48
Sift
Uncertain
0.0070
D
Sift4G
Uncertain
0.039
D
Polyphen
0.79
P
Vest4
0.55
MutPred
0.23
Loss of glycosylation at P117 (P = 0.0901);
MVP
0.86
MPC
0.29
ClinPred
0.72
D
GERP RS
4.5
Varity_R
0.37
gMVP
0.24

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs746797445; hg19: chr7-15725681; API