5-94871335-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024717.7(MCTP1):c.2119G>A(p.Val707Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000994 in 1,610,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
MCTP1
NM_024717.7 missense
NM_024717.7 missense
Scores
1
7
11
Clinical Significance
Conservation
PhyloP100: 5.56
Genes affected
MCTP1 (HGNC:26183): (multiple C2 and transmembrane domain containing 1) Enables calcium ion binding activity. Predicted to be involved in several processes, including modulation of chemical synaptic transmission; negative regulation of endocytosis; and negative regulation of response to oxidative stress. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.2983446).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCTP1 | NM_024717.7 | c.2119G>A | p.Val707Ile | missense_variant | 14/23 | ENST00000515393.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCTP1 | ENST00000515393.6 | c.2119G>A | p.Val707Ile | missense_variant | 14/23 | 1 | NM_024717.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151510Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250806Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135556
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GnomAD4 exome AF: 0.00000891 AC: 13AN: 1458534Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 725802
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151510Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73920
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.2119G>A (p.V707I) alteration is located in exon 14 (coding exon 14) of the MCTP1 gene. This alteration results from a G to A substitution at nucleotide position 2119, causing the valine (V) at amino acid position 707 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;.;.;T;T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.;.;.;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D;D;D;D
Sift4G
Benign
T;T;T;T;.;T;T;T
Polyphen
B;B;.;B;.;.;.;.
Vest4
MutPred
Gain of catalytic residue at L712 (P = 0.0826);.;.;.;.;.;.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at