SNX30

protein-coding

sorting nexin family member 30, the group of Autophagy related|PX-BAR domain containing|Sorting nexins

Gene summary

Predicted to enable phosphatidylinositol binding activity. Involved in positive regulation of autophagosome assembly and protein transport. Is active in early endosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001012994.2

Inheritance

—

ClinVar variants

U:64B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr9:112,750,760-112,881,671

External References & Databases

Ensembl (ENSG00000148158)

Transcript & Mutation Effects

hg38 • Region Span ~130.9 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 SNX30 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012994.2. 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			5 clinvar			5
missense			59 clinvar	1 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	1	0	65

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_001012994.2	RefSeq	NP_001013012.1	9	MANE Select
ENST00000374232.8	Ensembl	ENSP00000363349.3	9	MANE Select
ENST00000416585.1	Ensembl	ENSP00000390454.1	4	Standard
ENST00000870319.1	Ensembl	ENSP00000540378.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport

Molecular Function

protein binding
phosphatidylinositol binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374232
Coding exons: 9
Length: 130834
Individuals with no LoFs: 124786
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 124793
p: 0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.888	203	242	0.839	0.0000134	2848
Missense (PolyPhen)		98	108.48	0.90341		1211
Synonymous	1.38	77	94.0	0.819	0.00000548	847
Loss of Function	3.33	4	20.1	0.199	0.00000108	248

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	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. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.0790
RVIS EVS: -0.45
RVIS percentile EVS: 24.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.324

Gene Damage Prediction

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