rs587777676

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_005876.5(SPEG):​c.8270G>T​(p.Gly2757Val) 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 pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SPEG
NM_005876.5 missense

Scores

11
7
1

Clinical Significance

Uncertain significance criteria provided, single submitter P:1U:1

Conservation

PhyloP100: 8.00
Variant links:
Genes affected
SPEG (HGNC:16901): (striated muscle enriched protein kinase) This gene encodes a protein with similarity to members of the myosin light chain kinase family. This protein family is required for myocyte cytoskeletal development. Along with the desmin gene, expression of this gene may be controlled by the desmin locus control region. Mutations in this gene are associated with centronuclear myopathy 5. [provided by RefSeq, Jun 2016]
ASIC4-AS1 (HGNC:40960): (ASIC4 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.853

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPEGNM_005876.5 linkc.8270G>T p.Gly2757Val missense_variant 35/41 ENST00000312358.12 NP_005867.3 Q15772-5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPEGENST00000312358.12 linkc.8270G>T p.Gly2757Val missense_variant 35/415 NM_005876.5 ENSP00000311684.7 Q15772-5
SPEGENST00000485813.5 linkn.7513G>T non_coding_transcript_exon_variant 33/395
ASIC4-AS1ENST00000429882.1 linkn.183-6765C>A intron_variant 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
38
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Myopathy, centronuclear, 5 Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMAug 07, 2014- -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 15, 2022This missense change has been observed in individual(s) with clinical features of SPEG-related conditions (PMID: 25087613). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2757 of the SPEG protein (p.Gly2757Val). ClinVar contains an entry for this variant (Variation ID: 144081). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.94
BayesDel_addAF
Pathogenic
0.29
D
BayesDel_noAF
Pathogenic
0.17
CADD
Pathogenic
28
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.49
T
Eigen
Pathogenic
0.83
Eigen_PC
Pathogenic
0.76
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Uncertain
0.91
D
M_CAP
Pathogenic
0.40
D
MetaRNN
Pathogenic
0.85
D
MetaSVM
Uncertain
0.011
D
MutationAssessor
Pathogenic
3.0
M
PrimateAI
Uncertain
0.78
T
PROVEAN
Pathogenic
-5.9
D
REVEL
Pathogenic
0.82
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.0030
D
Polyphen
1.0
D
Vest4
0.95
MutPred
0.39
Loss of disorder (P = 0.0495);
MVP
0.59
MPC
1.1
ClinPred
1.0
D
GERP RS
4.4
Varity_R
0.78
gMVP
0.81

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: rs587777676; hg19: chr2-220353896; API