rs199872271

Variant summary

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

The NM_014748.4(SNX17):​c.817C>G​(p.Arg273Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. R273C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

SNX17
NM_014748.4 missense

Scores

9
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.27
Variant links:
Genes affected
SNX17 (HGNC:14979): (sorting nexin 17) 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 protein does not contain a coiled coil region, like some family members, but contains a B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]

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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
SNX17NM_014748.4 linkc.817C>G p.Arg273Gly missense_variant Exon 10 of 15 ENST00000233575.7 NP_055563.1 Q15036-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX17ENST00000233575.7 linkc.817C>G p.Arg273Gly missense_variant Exon 10 of 15 1 NM_014748.4 ENSP00000233575.2 Q15036-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
-0.052
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.20
.;T
Eigen
Benign
-0.20
Eigen_PC
Benign
0.013
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.93
D;D
M_CAP
Benign
0.011
T
MetaRNN
Uncertain
0.45
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.55
.;N
PrimateAI
Uncertain
0.63
T
PROVEAN
Uncertain
-2.7
D;D
REVEL
Benign
0.16
Sift
Uncertain
0.014
D;D
Sift4G
Uncertain
0.016
D;D
Polyphen
0.0040
.;B
Vest4
0.57
MutPred
0.50
.;Gain of helix (P = 0.0325);
MVP
0.46
MPC
0.25
ClinPred
0.95
D
GERP RS
5.0
Varity_R
0.40
gMVP
0.69

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: rs199872271; hg19: chr2-27598415; API