NM_020753.5:c.3565A>G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_020753.5(CASKIN2):c.3565A>G(p.Met1189Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,440,614 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
CASKIN2
NM_020753.5 missense
NM_020753.5 missense
Scores
4
13
1
Clinical Significance
Conservation
PhyloP100: 7.79
Publications
0 publications found
Genes affected
CASKIN2 (HGNC:18200): (CASK interacting protein 2) This gene encodes a large protein that contains six ankyrin repeats, as well as a Src homology 3 (SH3) domain and two sterile alpha motif (SAM) domains, which may be involved in protein-protein interactions. The C-terminal portion of this protein is proline-rich and contains a conserved region. A related protein interacts with calcium/calmodulin-dependent serine protein kinase (CASK). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020753.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CASKIN2 | TSL:1 MANE Select | c.3565A>G | p.Met1189Val | missense | Exon 20 of 20 | ENSP00000325355.3 | Q8WXE0-1 | ||
| CASKIN2 | c.3628A>G | p.Met1210Val | missense | Exon 20 of 20 | ENSP00000531972.1 | ||||
| CASKIN2 | c.3628A>G | p.Met1210Val | missense | Exon 20 of 20 | ENSP00000531973.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1440614Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 714380 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1440614
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
714380
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33174
American (AMR)
AF:
AC:
0
AN:
41392
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25720
East Asian (EAS)
AF:
AC:
0
AN:
38806
South Asian (SAS)
AF:
AC:
0
AN:
82910
European-Finnish (FIN)
AF:
AC:
0
AN:
51524
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1101674
Other (OTH)
AF:
AC:
1
AN:
59658
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of disorder (P = 0.0155)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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