NM_180991.5:c.1724C>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_180991.5(SLCO4C1):c.1724C>A(p.Ala575Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,598,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/24 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A575V) has been classified as Uncertain significance.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
SLCO4C1
NM_180991.5 missense
NM_180991.5 missense
Scores
19
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.545
Publications
0 publications found
Genes affected
SLCO4C1 (HGNC:23612): (solute carrier organic anion transporter family member 4C1) SLCO4C1 belongs to the organic anion transporter (OATP) family. OATPs are involved in the membrane transport of bile acids, conjugated steroids, thyroid hormone, eicosanoids, peptides, and numerous drugs in many tissues (Mikkaichi et al., 2004 [PubMed 14993604]).[supplied by OMIM, Mar 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLCO4C1 | NM_180991.5 | c.1724C>A | p.Ala575Glu | missense_variant | Exon 10 of 13 | ENST00000310954.7 | NP_851322.3 | |
| SLCO4C1 | XM_011543370.3 | c.1460C>A | p.Ala487Glu | missense_variant | Exon 9 of 12 | XP_011541672.1 | ||
| SLCO4C1 | XM_011543372.2 | c.1310C>A | p.Ala437Glu | missense_variant | Exon 12 of 15 | XP_011541674.1 | ||
| SLCO4C1 | XM_047417146.1 | c.1310C>A | p.Ala437Glu | missense_variant | Exon 12 of 15 | XP_047273102.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152054
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1446700Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 717894 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1446700
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
717894
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33298
American (AMR)
AF:
AC:
0
AN:
44518
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25806
East Asian (EAS)
AF:
AC:
1
AN:
39342
South Asian (SAS)
AF:
AC:
0
AN:
84000
European-Finnish (FIN)
AF:
AC:
0
AN:
53036
Middle Eastern (MID)
AF:
AC:
0
AN:
5716
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1101334
Other (OTH)
AF:
AC:
0
AN:
59650
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000658 AC: 1AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74278 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
152054
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74278
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
41418
American (AMR)
AF:
AC:
0
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
1
AN:
5188
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67992
Other (OTH)
AF:
AC:
0
AN:
2090
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of solvent accessibility (P = 0.0789);
MVP
MPC
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
DS_DG_spliceai
Position offset: 4
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.