rs138714955

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006755.2(TALDO1):​c.96C>A​(p.His32Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,421,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

TALDO1
NM_006755.2 missense, splice_region

Scores

1
3
15
Splicing: ADA: 0.01170
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280
Variant links:
Genes affected
TALDO1 (HGNC:11559): (transaldolase 1) Transaldolase 1 is a key enzyme of the nonoxidative pentose phosphate pathway providing ribose-5-phosphate for nucleic acid synthesis and NADPH for lipid biosynthesis. This pathway can also maintain glutathione at a reduced state and thus protect sulfhydryl groups and cellular integrity from oxygen radicals. The functional gene of transaldolase 1 is located on chromosome 11 and a pseudogene is identified on chromosome 1 but there are conflicting map locations. The second and third exon of this gene were developed by insertion of a retrotransposable element. This gene is thought to be involved in multiple sclerosis. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22299466).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TALDO1NM_006755.2 linkc.96C>A p.His32Gln missense_variant, splice_region_variant Exon 1 of 8 ENST00000319006.8 NP_006746.1 P37837-1A0A140VK56

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TALDO1ENST00000319006.8 linkc.96C>A p.His32Gln missense_variant, splice_region_variant Exon 1 of 8 1 NM_006755.2 ENSP00000321259.3 P37837-1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD3 exomes
AF:
0.00000536
AC:
1
AN:
186444
Hom.:
0
AF XY:
0.00000978
AC XY:
1
AN XY:
102298
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000413
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000141
AC:
2
AN:
1421100
Hom.:
0
Cov.:
31
AF XY:
0.00000284
AC XY:
2
AN XY:
705034
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000124
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.13e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
15
DANN
Uncertain
0.98
DEOGEN2
Benign
0.31
T;.
Eigen
Benign
-0.60
Eigen_PC
Benign
-0.47
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Benign
0.82
T;T
M_CAP
Pathogenic
0.79
D
MetaRNN
Benign
0.22
T;T
MetaSVM
Benign
-0.66
T
MutationAssessor
Benign
-1.0
N;.
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
1.0
N;N
REVEL
Benign
0.18
Sift
Benign
0.13
T;T
Sift4G
Benign
0.21
T;T
Polyphen
0.0
B;B
Vest4
0.22
MutPred
0.35
Gain of disorder (P = 0.0752);Gain of disorder (P = 0.0752);
MVP
0.79
MPC
0.071
ClinPred
0.17
T
GERP RS
1.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.8
Varity_R
0.10
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.012
dbscSNV1_RF
Benign
0.19
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs138714955; hg19: chr11-747577; API