16-70251143-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_058219.3(EXOSC6):​c.758C>T​(p.Pro253Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000592 in 1,538,016 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000065 ( 0 hom. )

Consequence

EXOSC6
NM_058219.3 missense

Scores

4
6
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.99
Variant links:
Genes affected
EXOSC6 (HGNC:19055): (exosome component 6) This gene product constitutes one of the subunits of the multisubunit particle called exosome, which mediates mRNA degradation. The composition of human exosome is similar to its yeast counterpart. This protein is homologous to the yeast Mtr3 protein. Its exact function is not known, however, it has been shown using a cell-free RNA decay system that the exosome is required for rapid degradation of unstable mRNAs containing AU-rich elements (AREs), but not for poly(A) shortening. The exosome does not recognize ARE-containing mRNAs on its own, but requires ARE-binding proteins that could interact with the exosome and recruit it to unstable mRNAs, thereby promoting their rapid degradation. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 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
EXOSC6NM_058219.3 linkc.758C>T p.Pro253Leu missense_variant Exon 1 of 1 ENST00000435634.3 NP_478126.1 Q5RKV6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EXOSC6ENST00000435634.3 linkc.758C>T p.Pro253Leu missense_variant Exon 1 of 1 6 NM_058219.3 ENSP00000398597.1 Q5RKV6

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152166
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000341
AC:
5
AN:
146618
Hom.:
0
AF XY:
0.0000120
AC XY:
1
AN XY:
83148
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:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000766
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000649
AC:
90
AN:
1385850
Hom.:
0
Cov.:
29
AF XY:
0.0000669
AC XY:
46
AN XY:
687350
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000802
Gnomad4 OTH exome
AF:
0.0000521
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152166
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000436
Hom.:
0
Bravo
AF:
0.0000113
ExAC
AF:
0.0000177
AC:
2

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 14, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.758C>T (p.P253L) alteration is located in exon 1 (coding exon 1) of the EXOSC6 gene. This alteration results from a C to T substitution at nucleotide position 758, causing the proline (P) at amino acid position 253 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.59
BayesDel_addAF
Benign
-0.035
T
BayesDel_noAF
Benign
-0.10
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.092
T
Eigen
Benign
0.0080
Eigen_PC
Benign
-0.071
FATHMM_MKL
Benign
0.74
D
LIST_S2
Benign
0.77
T
M_CAP
Pathogenic
0.80
D
MetaRNN
Uncertain
0.59
D
MetaSVM
Benign
-0.37
T
MutationAssessor
Uncertain
2.1
M
PrimateAI
Pathogenic
0.93
D
PROVEAN
Pathogenic
-6.3
D
REVEL
Uncertain
0.43
Sift
Uncertain
0.0030
D
Sift4G
Uncertain
0.015
D
Polyphen
0.97
D
Vest4
0.47
MutPred
0.36
Loss of disorder (P = 0.0523);
MVP
0.92
MPC
1.6
ClinPred
0.82
D
GERP RS
3.0
Varity_R
0.77
gMVP
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs752107411; hg19: chr16-70285046; API