rs1751034
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005845.5(ABCC4):āc.3348G>Cā(p.Lys1116Asn) 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 pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 29)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ABCC4
NM_005845.5 missense
NM_005845.5 missense
Scores
1
7
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.423
Genes affected
ABCC4 (HGNC:55): (ATP binding cassette subfamily C member 4 (PEL blood group)) The 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 MRP subfamily which is involved in multi-drug resistance. This family member plays a role in cellular detoxification as a pump for its substrate, organic anions. It may also function in prostaglandin-mediated cAMP signaling in ciliogenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.805
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC4 | NM_005845.5 | c.3348G>C | p.Lys1116Asn | missense_variant | 26/31 | ENST00000645237.2 | |
ABCC4 | NM_001301829.2 | c.3207G>C | p.Lys1069Asn | missense_variant | 25/30 | ||
ABCC4 | XM_047430034.1 | c.3219G>C | p.Lys1073Asn | missense_variant | 26/31 | ||
ABCC4 | XM_047430035.1 | c.2799G>C | p.Lys933Asn | missense_variant | 23/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC4 | ENST00000645237.2 | c.3348G>C | p.Lys1116Asn | missense_variant | 26/31 | NM_005845.5 | P1 | ||
ABCC4 | ENST00000646439.1 | c.3207G>C | p.Lys1069Asn | missense_variant | 25/30 | ||||
ABCC4 | ENST00000643051.1 | c.*973G>C | 3_prime_UTR_variant, NMD_transcript_variant | 27/33 | |||||
ABCC4 | ENST00000643842.1 | c.*3394G>C | 3_prime_UTR_variant, NMD_transcript_variant | 27/32 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 genomes
?
Cov.:
29
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1461634Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0AN XY: 727102
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1461634
Hom.:
Cov.:
42
AF XY:
AC XY:
0
AN XY:
727102
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 29
GnomAD4 genome
?
Cov.:
29
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
N;N;.
MutationTaster
Benign
P;P
PrimateAI
Uncertain
T
Polyphen
P;P;P
Vest4
0.22
MutPred
Loss of catalytic residue at M1117 (P = 0.0361);Loss of catalytic residue at M1117 (P = 0.0361);.;
MVP
0.71
MPC
0.40
ClinPred
D
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