chr15-85533870-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007200.5(AKAP13):c.468G>C(p.Gln156His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
AKAP13
NM_007200.5 missense
NM_007200.5 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: 0.321
Genes affected
AKAP13 (HGNC:371): (A-kinase anchoring protein 13) The A-kinase anchor proteins (AKAPs) are a group of structurally diverse proteins which have the common function of binding to the regulatory subunit of protein kinase A (PKA) and confining the holoenzyme to discrete locations within the cell. This gene encodes a member of the AKAP family. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms containing c-terminal dbl oncogene homology (DH) and pleckstrin homology (PH) domains. The DH domain is associated with guanine nucleotide exchange activation for the Rho/Rac family of small GTP binding proteins, resulting in the conversion of the inactive GTPase to the active form capable of transducing signals. The PH domain has multiple functions. Therefore, these isoforms function as scaffolding proteins to coordinate a Rho signaling pathway, function as protein kinase A-anchoring proteins and, in addition, enhance ligand-dependent activity of estrogen receptors alpha and beta. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.04168442).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP13 | NM_007200.5 | c.468G>C | p.Gln156His | missense_variant | 4/37 | ENST00000394518.7 | |
AKAP13 | NM_006738.6 | c.468G>C | p.Gln156His | missense_variant | 4/37 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP13 | ENST00000394518.7 | c.468G>C | p.Gln156His | missense_variant | 4/37 | 1 | NM_007200.5 | A2 | |
AKAP13 | ENST00000361243.6 | c.468G>C | p.Gln156His | missense_variant | 4/37 | 1 | A2 | ||
AKAP13 | ENST00000560302.5 | c.468G>C | p.Gln156His | missense_variant | 4/4 | 1 | |||
AKAP13 | ENST00000559362.5 | c.468G>C | p.Gln156His | missense_variant | 4/15 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
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 | Aug 17, 2022 | The c.468G>C (p.Q156H) alteration is located in exon 4 (coding exon 3) of the AKAP13 gene. This alteration results from a G to C substitution at nucleotide position 468, causing the glutamine (Q) at amino acid position 156 to be replaced by a histidine (H). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.0040, 0.0060, 0.010
.;B;B;B
Vest4
0.073, 0.21, 0.22
MutPred
Gain of catalytic residue at D160 (P = 0.1159);Gain of catalytic residue at D160 (P = 0.1159);Gain of catalytic residue at D160 (P = 0.1159);Gain of catalytic residue at D160 (P = 0.1159);
MVP
MPC
0.036
ClinPred
T
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
No publications associated with this variant yet.