1-15659912-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006511.3(RSC1A1):​c.44G>T​(p.Arg15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,453,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 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. R15H) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

RSC1A1
NM_006511.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.910

Publications

0 publications found
Variant links:
Genes affected
RSC1A1 (HGNC:10458): (regulator of solute carriers 1) The protein encoded by this intronless gene inhibits the expression of the solute carrier family 5 (sodium/glucose cotransporter), member 1 gene (SLC5A1) and downregulates exocytosis of the SLC5A1 protein. The encoded protein is sometimes found coating the trans-Golgi network and other times is localized to the nucleus, depending on the cell cycle stage. This protein also inhibits the expression of solute carrier family 22 (organic cation transporter), member 2 (SLC22A2). [provided by RefSeq, Dec 2015]
DDI2 (HGNC:24578): (DNA damage inducible 1 homolog 2) Enables aspartic-type endopeptidase activity; identical protein binding activity; and ubiquitin binding activity. Involved in several processes, including cellular response to hydroxyurea; proteolysis; and regulation of DNA stability. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.058341086).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RSC1A1NM_006511.3 linkc.44G>T p.Arg15Leu missense_variant Exon 1 of 1 ENST00000345034.2 NP_006502.1 Q92681
DDI2NM_032341.5 linkc.*122G>T 3_prime_UTR_variant Exon 10 of 10 ENST00000480945.6 NP_115717.3 Q5TDH0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RSC1A1ENST00000345034.2 linkc.44G>T p.Arg15Leu missense_variant Exon 1 of 1 6 NM_006511.3 ENSP00000341963.1 Q92681
DDI2ENST00000480945.6 linkc.*122G>T 3_prime_UTR_variant Exon 10 of 10 2 NM_032341.5 ENSP00000417748.1 Q5TDH0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.88e-7
AC:
1
AN:
1453456
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
722928
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33004
American (AMR)
AF:
0.00
AC:
0
AN:
42150
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25490
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39684
South Asian (SAS)
AF:
0.0000118
AC:
1
AN:
84534
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53242
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5712
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1109620
Other (OTH)
AF:
0.00
AC:
0
AN:
60020
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
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
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.097
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
15
DANN
Uncertain
0.99
DEOGEN2
Benign
0.42
T
Eigen
Benign
-0.76
Eigen_PC
Benign
-0.63
FATHMM_MKL
Benign
0.75
D
LIST_S2
Benign
0.69
T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.058
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
N
PhyloP100
0.91
PrimateAI
Benign
0.20
T
PROVEAN
Uncertain
-2.4
N
REVEL
Benign
0.14
Sift
Uncertain
0.027
D
Sift4G
Benign
0.081
T
Polyphen
0.044
B
Vest4
0.20
MutPred
0.16
Loss of phosphorylation at S17 (P = 0.072);
MVP
0.41
MPC
0.039
ClinPred
0.41
T
GERP RS
-1.6
PromoterAI
-0.0077
Neutral
Varity_R
0.077
gMVP
0.21
Mutation Taster
=92/8
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs761070050; hg19: chr1-15986407; API