4-3493040-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_173660.5(DOK7):ā€‹c.1054C>Gā€‹(p.Leu352Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000704 in 1,420,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 34)
Exomes š‘“: 7.0e-7 ( 0 hom. )

Consequence

DOK7
NM_173660.5 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.75
Variant links:
Genes affected
DOK7 (HGNC:26594): (docking protein 7) The protein encoded by this gene is essential for neuromuscular synaptogenesis. The protein functions in aneural activation of muscle-specific receptor kinase, which is required for postsynaptic differentiation, and in the subsequent clustering of the acetylcholine receptor in myotubes. This protein can also induce autophosphorylation of muscle-specific receptor kinase. Mutations in this gene are a cause of familial limb-girdle myasthenia autosomal recessive, which is also known as congenital myasthenic syndrome type 1B. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12748381).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DOK7NM_173660.5 linkuse as main transcriptc.1054C>G p.Leu352Val missense_variant 7/7 ENST00000340083.6 NP_775931.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DOK7ENST00000340083.6 linkuse as main transcriptc.1054C>G p.Leu352Val missense_variant 7/71 NM_173660.5 ENSP00000344432 P1Q18PE1-1
DOK7ENST00000643608.1 linkuse as main transcriptc.622C>G p.Leu208Val missense_variant 5/8 ENSP00000495701
DOK7ENST00000515886.5 linkuse as main transcriptc.124C>G p.Leu42Val missense_variant 4/42 ENSP00000492194
DOK7ENST00000507039.5 linkuse as main transcriptc.*275C>G 3_prime_UTR_variant 7/72 ENSP00000423614 Q18PE1-4

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
7.04e-7
AC:
1
AN:
1420670
Hom.:
0
Cov.:
111
AF XY:
0.00
AC XY:
0
AN XY:
704386
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:
9.12e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

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

Submissions by phenotype

Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJul 25, 2022This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 352 of the DOK7 protein (p.Leu352Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DOK7-related conditions. ClinVar contains an entry for this variant (Variation ID: 534114). 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: "Benign"; Align-GVGD: "Class C0"). 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
18
DANN
Benign
0.84
DEOGEN2
Benign
0.11
T;.;.
Eigen
Benign
-0.54
Eigen_PC
Benign
-0.48
FATHMM_MKL
Benign
0.67
D
LIST_S2
Uncertain
0.91
D;D;D
M_CAP
Benign
0.048
D
MetaRNN
Benign
0.13
T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
0.69
N;.;.
MutationTaster
Benign
1.0
D;N;N
PrimateAI
Uncertain
0.66
T
PROVEAN
Benign
-0.97
N;.;.
REVEL
Benign
0.081
Sift
Uncertain
0.022
D;.;.
Sift4G
Benign
0.15
T;.;.
Polyphen
0.020
B;.;.
Vest4
0.12
MutPred
0.23
Gain of catalytic residue at L352 (P = 0.0123);.;.;
MVP
0.53
MPC
0.0045
ClinPred
0.32
T
GERP RS
2.5
Varity_R
0.16
gMVP
0.17

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: rs1037224921; hg19: chr4-3494767; API