SNX32

protein-coding

sorting nexin 32, the group of PX-BAR domain containing|Sorting nexins

Gene summary

Predicted to enable dynactin binding activity and phosphatidylinositol binding activity. Involved in endosome to lysosome transport via multivesicular body sorting pathway. Located in endosome; plasma membrane; and trans-Golgi network. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SNX6B

MANE transcript

NM_152760.3

Inheritance

—

ClinVar variants

U:90B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr11:65,833,834-65,856,896

External References & Databases

Ensembl (ENSG00000172803)

Transcript & Mutation Effects

hg38 • Region Span ~23.1 kb

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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 SNX32 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 90

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152760.3. 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						0
missense			89 clinvar	2 clinvar		91
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	90	2	0	92

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152760.3	RefSeq	NP_689973.2	13	MANE Select
ENST00000308342.7	Ensembl	ENSP00000310620.6	13	MANE Select
ENST00000913492.1	Ensembl	ENSP00000583551.1	13	Standard
ENST00000913492.2	Ensembl	ENSP00000583551.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)

Biological Process

protein transport
regulation of macroautophagy

Molecular Function

protein binding
phosphatidylinositol binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308342
Coding exons: 13
Length: 23256
Individuals with no LoFs: 125552
Homozygous LoFs: 1
Heterozygous LoFs: 195
Defined: 125748
p: 0.000780

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.259	275	263	1.04	0.0000185	2619
Missense (PolyPhen)		70	64.62	1.0833		707
Synonymous	-2.36	143	111	1.28	0.00000759	801
Loss of Function	-0.0711	27	26.6	1.01	0.00000161	275

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.0017	0.0017	notable
Finnish	0.00029	0.00028	rare
European (Non-Finnish)	0.00063	0.00062	rare
South Asian	0.0011	0.0011	notable
Other	0.0011	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in several stages of intracellular trafficking. {ECO:0000250}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.920
RVIS EVS: -0.82
RVIS percentile EVS: 11.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.683

Gene Damage Prediction

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