SNX13

protein-coding

sorting nexin 13, the group of Sorting nexins

Gene summary

This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]

MANE transcript

NM_015132.5

Inheritance

—

ClinVar variants

U:119B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr7:17,790,761-17,940,501

External References & Databases

Ensembl (ENSG00000071189)

Transcript & Mutation Effects

hg38 • Region Span ~149.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNX13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015132.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			9 clinvar	2 clinvar	1 clinvar	12
missense			105 clinvar	3 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	119	5	1	125

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015132.5	RefSeq	NP_055947.1	26	MANE Select
ENST00000428135.7	Ensembl	ENSP00000398789.2	26	MANE Select
NM_001350862.2	RefSeq	NP_001337791.1	26	Standard
NM_001350863.2	RefSeq	NP_001337792.1	23	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
snx13	Danio rerio	Structure: cardiac muscle cell Quality: apoptotic abnormal

Gene / Model

Organism

Observed Phenotype

snx13

Danio rerio

Structure: cardiac muscle cell

Quality: apoptotic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
negative regulation of signal transduction
positive regulation of GTPase activity

Molecular Function

phosphatidylinositol-3-phosphate binding
phosphatidylinositol binding

Cellular Component

early endosome
early endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000428135
Coding exons: 26
Length: 149740
Individuals with no LoFs: 124607
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 124623
p: 0.0000642

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.99	336	455	0.738	0.0000235	6257
Missense (PolyPhen)		73	135.99	0.53682		1885
Synonymous	-1.56	173	149	1.16	0.00000723	1684
Loss of Function	5.25	12	53.4	0.225	0.00000283	734

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000083	0.000080	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in several stages of intracellular trafficking. May play a role in endosome homeostasis (By similarity). Acts as a GAP for Galphas. {ECO:0000250, ECO:0000269|PubMed:11729322}.;

Recessive Scores

pRec: 0.132

Intolerance Scores

LoFtool: 0.523
RVIS EVS: -0.44
RVIS percentile EVS: 24.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.700

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium