chr15-64112666-C-T

Variant summary

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

The NM_003099.5(SNX1):​c.253C>T​(p.Pro85Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)

Consequence

SNX1
NM_003099.5 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.08
Variant links:
Genes affected
SNX1 (HGNC:11172): (sorting nexin 1) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This endosomal protein regulates the cell-surface expression of epidermal growth factor receptor. This protein also has a role in sorting protease-activated receptor-1 from early endosomes to lysosomes. This protein may form oligomeric complexes with family members. This gene results in three transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

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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=0.1638492).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX1NM_003099.5 linkc.253C>T p.Pro85Ser missense_variant Exon 2 of 15 ENST00000559844.6 NP_003090.2 Q13596-1
SNX1NM_001242933.2 linkc.253C>T p.Pro85Ser missense_variant Exon 2 of 15 NP_001229862.1 Q13596-3
SNX1NM_148955.4 linkc.253C>T p.Pro85Ser missense_variant Exon 2 of 13 NP_683758.1 Q13596-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX1ENST00000559844.6 linkc.253C>T p.Pro85Ser missense_variant Exon 2 of 15 1 NM_003099.5 ENSP00000453785.1 Q13596-1

Frequencies

GnomAD3 genomes
AF:
0.0000132
AC:
2
AN:
151962
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000484
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
GnomAD4 exome
Cov.:
29
GnomAD4 genome
AF:
0.0000132
AC:
2
AN:
151962
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.0000484
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
Bravo
AF:
0.00000756

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Dec 02, 2022
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.253C>T (p.P85S) alteration is located in exon 2 (coding exon 2) of the SNX1 gene. This alteration results from a C to T substitution at nucleotide position 253, causing the proline (P) at amino acid position 85 to be replaced by a serine (S). 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
Benign
0.070
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
21
DANN
Benign
0.97
DEOGEN2
Benign
0.19
.;T;T;.;T
Eigen
Benign
-0.33
Eigen_PC
Benign
-0.15
FATHMM_MKL
Benign
0.63
D
LIST_S2
Benign
0.79
T;T;D;D;D
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.16
T;T;T;T;T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
1.1
L;L;.;L;.
PrimateAI
Benign
0.45
T
PROVEAN
Uncertain
-2.5
N;N;.;N;D
REVEL
Benign
0.10
Sift
Uncertain
0.024
D;T;.;T;D
Sift4G
Benign
0.19
T;T;D;T;T
Polyphen
0.087, 0.045
.;B;.;B;.
Vest4
0.34
MutPred
0.56
Gain of phosphorylation at P85 (P = 0.0571);Gain of phosphorylation at P85 (P = 0.0571);Gain of phosphorylation at P85 (P = 0.0571);Gain of phosphorylation at P85 (P = 0.0571);.;
MVP
0.26
MPC
0.28
ClinPred
0.41
T
GERP RS
4.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.096
gMVP
0.18

Splicing

Name
Calibrated prediction
Score
Prediction
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: rs1173278342; hg19: chr15-64404865; API