NM_001099646.3:c.1177G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001099646.3(SLC47A2):c.1177G>A(p.Gly393Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00614 in 1,612,630 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0063 ( 48 hom. )
Consequence
SLC47A2
NM_001099646.3 missense
NM_001099646.3 missense
Scores
4
5
9
Clinical Significance
Conservation
PhyloP100: 1.54
Publications
23 publications found
Genes affected
SLC47A2 (HGNC:26439): (solute carrier family 47 member 2) This gene encodes a protein belonging to a family of transporters involved in excretion of toxic electrolytes, both endogenous and exogenous, through urine and bile. This transporter family shares homology with the bacterial MATE (multidrug and toxin extrusion) protein family responsible for drug resistance. This gene is one of two members of the MATE transporter family located near each other on chromosome 17. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
ALDH3A2 (HGNC:403): (aldehyde dehydrogenase 3 family member A2) Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
ALDH3A2 Gene-Disease associations (from GenCC):
- Sjogren-Larsson syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Myriad Women’s Health, PanelApp Australia, Labcorp Genetics (formerly Invitae), Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.024230838).
BP6
Variant 17-19681658-C-T is Benign according to our data. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-19681658-C-T is described in CliVar as Benign. Clinvar id is 3387889.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.0063 (9204/1460360) while in subpopulation MID AF = 0.0283 (163/5768). AF 95% confidence interval is 0.0247. There are 48 homozygotes in GnomAdExome4. There are 4860 alleles in the male GnomAdExome4 subpopulation. Median coverage is 31. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC47A2 | NM_001099646.3 | c.1177G>A | p.Gly393Arg | missense_variant | Exon 14 of 17 | ENST00000433844.4 | NP_001093116.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00456 AC: 694AN: 152152Hom.: 5 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
694
AN:
152152
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:
GnomAD2 exomes AF: 0.00600 AC: 1499AN: 249926 AF XY: 0.00676 show subpopulations
GnomAD2 exomes
AF:
AC:
1499
AN:
249926
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00630 AC: 9204AN: 1460360Hom.: 48 Cov.: 31 AF XY: 0.00669 AC XY: 4860AN XY: 726318 show subpopulations
GnomAD4 exome
AF:
AC:
9204
AN:
1460360
Hom.:
Cov.:
31
AF XY:
AC XY:
4860
AN XY:
726318
show subpopulations
African (AFR)
AF:
AC:
36
AN:
33452
American (AMR)
AF:
AC:
171
AN:
44658
Ashkenazi Jewish (ASJ)
AF:
AC:
144
AN:
26036
East Asian (EAS)
AF:
AC:
0
AN:
39680
South Asian (SAS)
AF:
AC:
1243
AN:
86118
European-Finnish (FIN)
AF:
AC:
35
AN:
53376
Middle Eastern (MID)
AF:
AC:
163
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
7009
AN:
1110930
Other (OTH)
AF:
AC:
403
AN:
60342
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
488
976
1464
1952
2440
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
260
520
780
1040
1300
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.00454 AC: 691AN: 152270Hom.: 5 Cov.: 32 AF XY: 0.00465 AC XY: 346AN XY: 74464 show subpopulations
GnomAD4 genome
AF:
AC:
691
AN:
152270
Hom.:
Cov.:
32
AF XY:
AC XY:
346
AN XY:
74464
show subpopulations
African (AFR)
AF:
AC:
40
AN:
41560
American (AMR)
AF:
AC:
83
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
21
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5182
South Asian (SAS)
AF:
AC:
61
AN:
4818
European-Finnish (FIN)
AF:
AC:
3
AN:
10614
Middle Eastern (MID)
AF:
AC:
7
AN:
294
European-Non Finnish (NFE)
AF:
AC:
453
AN:
68004
Other (OTH)
AF:
AC:
14
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
38
75
113
150
188
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
27
ALSPAC
AF:
AC:
21
ESP6500AA
AF:
AC:
1
ESP6500EA
AF:
AC:
58
ExAC
AF:
AC:
737
Asia WGS
AF:
AC:
15
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
SLC47A2: BP4, BS1, BS2 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;.
PhyloP100
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Pathogenic
D;D
Polyphen
D;D
Vest4
MutPred
Loss of catalytic residue at V430 (P = 0.0432);.;
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
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.