NM_001348946.2:c.3322T>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_001348946.2(ABCB1):c.3322T>A(p.Trp1108Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
ABCB1
NM_001348946.2 missense
NM_001348946.2 missense
Scores
8
6
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 9.31
Publications
0 publications found
Genes affected
ABCB1 (HGNC:40): (ATP binding cassette subfamily B member 1) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is an ATP-dependent drug efflux pump for xenobiotic compounds with broad substrate specificity. It is responsible for decreased drug accumulation in multidrug-resistant cells and often mediates the development of resistance to anticancer drugs. This protein also functions as a transporter in the blood-brain barrier. Mutations in this gene are associated with colchicine resistance and Inflammatory bowel disease 13. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.756
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ABCB1 | NM_001348946.2 | c.3322T>A | p.Trp1108Arg | missense_variant | Exon 26 of 28 | ENST00000622132.5 | NP_001335875.1 | |
| ABCB1 | NM_001348945.2 | c.3532T>A | p.Trp1178Arg | missense_variant | Exon 30 of 32 | NP_001335874.1 | ||
| ABCB1 | NM_000927.5 | c.3322T>A | p.Trp1108Arg | missense_variant | Exon 27 of 29 | NP_000918.2 | ||
| ABCB1 | NM_001348944.2 | c.3322T>A | p.Trp1108Arg | missense_variant | Exon 28 of 30 | NP_001335873.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 35
GnomAD4 exome
Cov.:
35
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;.;T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
N;N;.
PhyloP100
PrimateAI
Pathogenic
T
PROVEAN
Pathogenic
.;D;D
REVEL
Pathogenic
Sift
Uncertain
.;D;T
Sift4G
Benign
T;T;T
Polyphen
D;D;.
Vest4
MutPred
Gain of methylation at W1108 (P = 0.0238);Gain of methylation at W1108 (P = 0.0238);.;
MVP
MPC
0.89
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
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