rs1215667615

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2

The NM_145269.5(CIBAR1):​c.400C>A​(p.Arg134Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

CIBAR1
NM_145269.5 missense

Scores

4
10
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.69
Variant links:
Genes affected
CIBAR1 (HGNC:30452): (CBY1 interacting BAR domain containing 1) Enables phospholipid binding activity. Involved in several processes, including inner mitochondrial membrane organization; limb morphogenesis; and membrane tubulation. Located in several cellular components, including centriole; ciliary base; and mitochondrial crista. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM1
In a mutagenesis_site Abolishes ability to induce membrane remodeling in the presence of CBY1; when associated with E-107; E-110; E-114; E-132 and E-136. (size 0) in uniprot entity CBAR1_HUMAN
PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CIBAR1NM_145269.5 linkc.400C>A p.Arg134Ser missense_variant Exon 4 of 9 ENST00000518322.6 NP_660312.2 A1XBS5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CIBAR1ENST00000518322.6 linkc.400C>A p.Arg134Ser missense_variant Exon 4 of 9 5 NM_145269.5 ENSP00000429367.1 A1XBS5-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000402
AC:
1
AN:
248520
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134854
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000329
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.97
BayesDel_addAF
Pathogenic
0.30
D
BayesDel_noAF
Pathogenic
0.19
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Benign
0.16
.;T;T;.;T;.;T;.;.
Eigen
Uncertain
0.56
Eigen_PC
Uncertain
0.61
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.97
D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.73
D;D;D;D;D;D;D;D;D
MetaSVM
Benign
-1.0
T
PrimateAI
Uncertain
0.72
T
PROVEAN
Pathogenic
-5.3
D;D;D;D;D;D;.;D;D
REVEL
Uncertain
0.41
Sift
Uncertain
0.0010
D;D;D;D;D;D;.;D;D
Sift4G
Uncertain
0.0030
D;D;D;D;D;D;D;D;D
Polyphen
0.99
.;.;D;.;.;.;.;.;.
Vest4
0.94, 0.90, 0.94, 0.96
MutPred
0.54
.;.;Gain of phosphorylation at R134 (P = 0.0203);Gain of phosphorylation at R134 (P = 0.0203);.;Gain of phosphorylation at R134 (P = 0.0203);Gain of phosphorylation at R134 (P = 0.0203);.;.;
MVP
0.77
MPC
0.65
ClinPred
0.99
D
GERP RS
5.7
Varity_R
0.84
gMVP
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs1215667615; hg19: chr8-94717206; API