chr2-55295654-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365480.1(CCDC88A):c.5494C>A(p.Pro1832Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
CCDC88A
NM_001365480.1 missense
NM_001365480.1 missense
Scores
2
12
3
Clinical Significance
Conservation
PhyloP100: 6.09
Genes affected
CCDC88A (HGNC:25523): (coiled-coil domain containing 88A) This gene encodes a member of the Girdin family of coiled-coil domain containing proteins. The encoded protein is an actin-binding protein that is activated by the serine/threonine kinase Akt and plays a role in cytoskeleton remodeling and cell migration. The encoded protein also enhances Akt signaling by mediating phosphoinositide 3-kinase (PI3K)-dependent activation of Akt by growth factor receptor tyrosine kinases and G protein-coupled receptors. Increased expression of this gene and phosphorylation of the encoded protein may play a role in cancer metastasis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC88A | NM_001365480.1 | c.5494C>A | p.Pro1832Thr | missense_variant | 31/33 | ENST00000436346.7 | |
CCDC88A | NM_001135597.2 | c.5491C>A | p.Pro1831Thr | missense_variant | 31/33 | ||
CCDC88A | NM_018084.5 | c.5410C>A | p.Pro1804Thr | missense_variant | 30/32 | ||
CCDC88A | NM_001254943.2 | c.5269C>A | p.Pro1757Thr | missense_variant | 32/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC88A | ENST00000436346.7 | c.5494C>A | p.Pro1832Thr | missense_variant | 31/33 | 5 | NM_001365480.1 | A1 | |
ENST00000625718.2 | n.86-13178G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
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 | Dec 19, 2022 | The c.5491C>A (p.P1831T) alteration is located in exon 31 (coding exon 31) of the CCDC88A gene. This alteration results from a C to A substitution at nucleotide position 5491, causing the proline (P) at amino acid position 1831 to be replaced by a threonine (T). 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
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;.;D;D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.;.;.;D;.;.;.;D;.;.;D
REVEL
Uncertain
Sift
Uncertain
D;D;.;.;.;D;.;.;.;D;.;.;D
Sift4G
Uncertain
D;D;.;.;.;D;.;.;.;D;.;.;T
Polyphen
D;D;D;D;.;D;.;.;.;.;.;.;.
Vest4
MutPred
0.39
.;.;.;Gain of sheet (P = 0.0028);.;Gain of sheet (P = 0.0028);.;.;.;.;.;.;.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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.