SNX25

protein-coding

sorting nexin 25, the group of Sorting nexins

Gene summary

Predicted to enable phosphatidylinositol binding activity. Involved in negative regulation of transforming growth factor beta receptor signaling pathway and receptor catabolic process. Predicted to be located in endosome membrane. Predicted to be active in endosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001378034.2

Inheritance

—

ClinVar variants

U:76B:3

Top phenotype

SNX25-related autism spectrum disorder

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr4:185,204,237-185,370,185

External References & Databases

Ensembl (ENSG00000109762)

Transcript & Mutation Effects

hg38 • Region Span ~165.9 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 SNX25 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 1

SNX25-related autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001378034.2. 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			1 clinvar	2 clinvar		3
missense			70 clinvar	1 clinvar		71
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	76	3	0	79

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 73 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001378034.2	RefSeq	NP_001364963.1	19	MANE Select
ENST00000652585.2	Ensembl	ENSP00000498676.1	19	MANE Select
NM_001317781.2	RefSeq	NP_001304710.1	18	Standard
NM_001378032.2	RefSeq	NP_001364961.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
negative regulation of transforming growth factor beta receptor signaling pathway
receptor catabolic process
negative regulation of pathway-restricted SMAD protein phosphorylation

Molecular Function

molecular_function
type I transforming growth factor beta receptor binding
phosphatidylinositol binding

Cellular Component

cellular_component
endosome membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000504273
Coding exons: 18
Length: 165949
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125748
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.416	415	440	0.944	0.0000223	5595
Missense (PolyPhen)		82	109.73	0.74729		1443
Synonymous	0.466	154	162	0.953	0.00000866	1484
Loss of Function	4.18	16	46.9	0.341	0.00000231	580

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00027	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0742

Intolerance Scores

LoFtool: 0.794
RVIS EVS: -0.17
RVIS percentile EVS: 40.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.104

Gene Damage Prediction

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