5-122803505-T-A

Position:

• chr5-122803505-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_003100.4(SNX2):​c.535T>A​(p.Ser179Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SNX2 NM_003100.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.11

Genes affected

SNX2 (HGNC:11173): (sorting nexin 2) This gene belongs to the sorting nexin family whose members contain the phosphoinositide-binding phox (PX) domain. The encoded protein is a component of the retromer complex which plays a role in protein sorting in the endocytic pathway. This protein may form oligomeric complexes with other family members. Alternate splicing results in multiple transcript variants of this gene. Pseudogenes associated with this gene are located on chromosomes 1 and 7. [provided by RefSeq, May 2013]

SNX2 (HGNC:):

ACMG classification

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=0.23570812).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX2	NM_003100.4	c.535T>A	p.Ser179Thr	missense_variant	6/15	ENST00000379516.7	NP_003091.2
SNX2	NM_001278199.1	c.184T>A	p.Ser62Thr	missense_variant	6/15		NP_001265128.1
LOC105379154	XR_007058917.1	n.1177-13899A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX2	ENST00000379516.7	c.535T>A	p.Ser179Thr	missense_variant	6/15	1	NM_003100.4	ENSP00000368831.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 28, 2022

The c.535T>A (p.S179T) alteration is located in exon 6 (coding exon 6) of the SNX2 gene. This alteration results from a T to A substitution at nucleotide position 535, causing the serine (S) at amino acid position 179 to be replaced by a threonine (T). 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	0.071
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	23
DANN	Benign	0.77
DEOGEN2	Benign	0.15	T;.;.
Eigen	Benign	-0.21
Eigen_PC	Benign	0.022
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.90	D;D;T
M_CAP	Benign	0.0082	T
MetaRNN	Benign	0.24	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.030	N;.;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.050	N;N;N
REVEL	Benign	0.054
Sift	Benign	0.53	T;T;T
Sift4G	Benign	0.72	T;T;T
Polyphen		0.0010	B;.;.
Vest4		0.17
MutPred		0.46		Loss of disorder (P = 0.0524);.;.;
MVP		0.33
MPC		0.17
ClinPred		0.76	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.13
gMVP		0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-122139200;