rs865782605

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_001370549.1(SLC16A11):​c.697G>T​(p.Gly233Trp) variant causes a missense change involving the alteration of a 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G233R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SLC16A11
NM_001370549.1 missense

Scores

7
10
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.57
Variant links:
Genes affected
SLC16A11 (HGNC:23093): (solute carrier family 16 member 11) Enables pyruvate transmembrane transporter activity. Involved in lipid metabolic process. Located in endoplasmic reticulum membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.903

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC16A11NM_001370549.1 linkc.697G>T p.Gly233Trp missense_variant Exon 4 of 5 ENST00000574600.3 NP_001357478.1
SLC16A11NM_153357.3 linkc.697G>T p.Gly233Trp missense_variant Exon 3 of 4 NP_699188.2 Q8NCK7
SLC16A11NM_001370553.1 linkc.697G>T p.Gly233Trp missense_variant Exon 4 of 4 NP_001357482.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC16A11ENST00000574600.3 linkc.697G>T p.Gly233Trp missense_variant Exon 4 of 5 3 NM_001370549.1 ENSP00000460927.2 I3L431
SLC16A11ENST00000573338.1 linkn.678-505G>T intron_variant Intron 1 of 1 1
SLC16A11ENST00000662352.3 linkc.697G>T p.Gly233Trp missense_variant Exon 3 of 4 ENSP00000499634.1 I3L431
SLC16A11ENST00000673828.2 linkc.697G>T p.Gly233Trp missense_variant Exon 4 of 4 ENSP00000501313.1 A0A669KBK5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1407640
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
695232
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.93
BayesDel_addAF
Pathogenic
0.22
D
BayesDel_noAF
Uncertain
0.080
CADD
Pathogenic
31
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.57
D;.
Eigen
Pathogenic
0.89
Eigen_PC
Pathogenic
0.83
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Benign
0.82
T;T
M_CAP
Uncertain
0.24
D
MetaRNN
Pathogenic
0.90
D;D
MetaSVM
Uncertain
-0.023
T
MutationAssessor
Uncertain
2.5
M;.
PrimateAI
Uncertain
0.73
T
PROVEAN
Pathogenic
-7.4
D;D
REVEL
Uncertain
0.54
Sift
Uncertain
0.0010
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
1.0
D;.
Vest4
0.82
MutPred
0.69
Gain of sheet (P = 0.1208);.;
MVP
0.76
MPC
1.2
ClinPred
1.0
D
GERP RS
5.1
Varity_R
0.88
gMVP
0.87

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

LitVar

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

Other links and lift over

dbSNP: rs865782605; hg19: chr17-6945732; API