NM_032415.7:c.590T>C

Variant summary

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

The NM_032415.7(CARD11):​c.590T>C​(p.Val197Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars). Synonymous variant affecting the same amino acid position (i.e. V197V) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

CARD11
NM_032415.7 missense

Scores

3
8
8

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 6.91
Variant links:
Genes affected
CARD11 (HGNC:16393): (caspase recruitment domain family member 11) The protein encoded by this gene belongs to the membrane-associated guanylate kinase (MAGUK) family, a class of proteins that functions as molecular scaffolds for the assembly of multiprotein complexes at specialized regions of the plasma membrane. This protein is also a member of the CARD protein family, which is defined by carrying a characteristic caspase-associated recruitment domain (CARD). This protein has a domain structure similar to that of CARD14 protein. The CARD domains of both proteins have been shown to specifically interact with BCL10, a protein known to function as a positive regulator of cell apoptosis and NF-kappaB activation. When expressed in cells, this protein activated NF-kappaB and induced the phosphorylation of BCL10. [provided by RefSeq, Jul 2008]
CARD11-AS1 (HGNC:40766): (CARD11 antisense RNA 1)

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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
CARD11NM_032415.7 linkc.590T>C p.Val197Ala missense_variant Exon 5 of 25 ENST00000396946.9 NP_115791.3 Q9BXL7A0A024R854Q8TES3
CARD11NM_001324281.3 linkc.590T>C p.Val197Ala missense_variant Exon 6 of 26 NP_001311210.1 Q9BXL7A0A024R854Q8TES3
CARD11-AS1NR_187443.1 linkn.272A>G non_coding_transcript_exon_variant Exon 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CARD11ENST00000396946.9 linkc.590T>C p.Val197Ala missense_variant Exon 5 of 25 1 NM_032415.7 ENSP00000380150.4 Q9BXL7

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link

Submissions by phenotype

not specified Other:1
Sep 19, 2013
ITMI
Significance: not provided
Review Status: no classification provided
Collection Method: reference population

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.82
BayesDel_addAF
Benign
-0.040
T
BayesDel_noAF
Benign
-0.30
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.50
T
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.48
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.77
T
M_CAP
Benign
0.025
T
MetaRNN
Uncertain
0.61
D
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.1
M
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
-2.3
N
REVEL
Benign
0.20
Sift
Uncertain
0.0070
D
Sift4G
Uncertain
0.044
D
Polyphen
0.98
D
Vest4
0.76
MutPred
0.32
Loss of stability (P = 2e-04);
MVP
0.34
MPC
2.3
ClinPred
0.95
D
GERP RS
4.2
Varity_R
0.31
gMVP
0.84

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: rs587778153; hg19: chr7-2983940; API