rs57521028

Variant summary

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

The NM_020902.2(CAMSAP3):​c.882C>A​(p.Tyr294*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

CAMSAP3
NM_020902.2 stop_gained

Scores

2
1
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0280
Variant links:
Genes affected
CAMSAP3 (HGNC:29307): (calmodulin regulated spectrin associated protein family member 3) Enables actin filament binding activity and microtubule minus-end binding activity. Involved in several processes, including microtubule cytoskeleton organization; regulation of organelle organization; and zonula adherens maintenance. Located in cytoplasm; nucleoplasm; and zonula adherens. Colocalizes with centrosome and microtubule minus-end. [provided by Alliance of Genome Resources, Apr 2022]

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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
CAMSAP3NM_020902.2 linkc.882C>A p.Tyr294* stop_gained Exon 6 of 17 ENST00000160298.9 NP_065953.1 Q9P1Y5-1
CAMSAP3NM_001080429.3 linkc.963C>A p.Tyr321* stop_gained Exon 8 of 19 NP_001073898.1 Q9P1Y5-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CAMSAP3ENST00000160298.9 linkc.882C>A p.Tyr294* stop_gained Exon 6 of 17 2 NM_020902.2 ENSP00000160298.3 Q9P1Y5-1
CAMSAP3ENST00000446248.4 linkc.963C>A p.Tyr321* stop_gained Exon 8 of 19 1 ENSP00000416797.1 Q9P1Y5-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.56
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
35
DANN
Uncertain
0.98
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.64
FATHMM_MKL
Benign
0.56
D
Vest4
0.45
GERP RS
-1.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.66
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.66
Position offset: -4

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: chr19-7675483; API