5-35910481-C-T

Variant summary

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

The NM_001042625.2(CAPSL):​c.200G>A​(p.Gly67Glu) 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 (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

CAPSL
NM_001042625.2 missense

Scores

11
7
1

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 7.38
Variant links:
Genes affected
CAPSL (HGNC:28375): (calcyphosine like) Predicted to enable calcium ion binding activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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, 0.861

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CAPSLNM_001042625.2 linkuse as main transcriptc.200G>A p.Gly67Glu missense_variant 3/5 ENST00000651391.1 NP_001036090.1 Q8WWF8
CAPSLNM_144647.4 linkuse as main transcriptc.200G>A p.Gly67Glu missense_variant 3/5 NP_653248.3 Q8WWF8
CAPSLXM_006714444.4 linkuse as main transcriptc.251G>A p.Gly84Glu missense_variant 3/5 XP_006714507.1
CAPSLXM_006714445.4 linkuse as main transcriptc.251G>A p.Gly84Glu missense_variant 3/5 XP_006714508.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CAPSLENST00000651391.1 linkuse as main transcriptc.200G>A p.Gly67Glu missense_variant 3/5 NM_001042625.2 ENSP00000498465.1 Q8WWF8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Autism Uncertain:1
Uncertain significance, no assertion criteria providedresearchCentre for Addiction & Mental Health, Centre for Addiction & Mental Health-Gene not previously associated with disease; independent supportng evidence needed -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.28
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.42
T;T;.;.
Eigen
Pathogenic
0.91
Eigen_PC
Pathogenic
0.84
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.94
.;D;D;D
M_CAP
Uncertain
0.14
D
MetaRNN
Pathogenic
0.86
D;D;D;D
MetaSVM
Uncertain
0.48
D
MutationAssessor
Pathogenic
3.2
M;M;.;.
PrimateAI
Pathogenic
0.80
T
PROVEAN
Pathogenic
-7.9
D;D;D;D
REVEL
Pathogenic
0.87
Sift
Uncertain
0.0010
D;D;D;D
Sift4G
Uncertain
0.0020
D;D;D;D
Polyphen
1.0
D;D;.;.
Vest4
0.96
MutPred
0.61
Loss of catalytic residue at D70 (P = 0.0662);Loss of catalytic residue at D70 (P = 0.0662);Loss of catalytic residue at D70 (P = 0.0662);Loss of catalytic residue at D70 (P = 0.0662);
MVP
0.93
MPC
0.16
ClinPred
1.0
D
GERP RS
5.3
Varity_R
0.99
gMVP
0.95

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-35910583; COSMIC: COSV68438109; API