SNX25

sorting nexin 25, the group of Sorting nexins

Basic information

Region (hg38): 4:185204236-185370185

Links

ENSG00000109762 ∙ NCBI:83891 ∙ ∙ HGNC:21883 ∙ Uniprot:Q9H3E2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNX25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX25 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			30	1		31
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in SNX25

This is a list of pathogenic ClinVar variants found in the SNX25 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-185258978-T-A		not specified	Uncertain significance (May 18, 2023)
4-185264547-C-G		not specified	Uncertain significance (May 27, 2022)
4-185264577-C-T		not specified	Uncertain significance (Aug 10, 2021)
4-185267038-C-T		not specified	Uncertain significance (Jun 19, 2024)
4-185267110-A-G		not specified	Uncertain significance (Nov 06, 2023)
4-185267112-C-T		not specified	Uncertain significance (Nov 22, 2023)
4-185267116-T-G		not specified	Uncertain significance (Oct 14, 2021)
4-185288013-T-C		not specified	Uncertain significance (Nov 05, 2021)
4-185320773-G-A		not specified	Uncertain significance (Aug 04, 2023)
4-185320784-G-T		SNX25-related autism spectrum disorder	Uncertain significance (Sep 03, 2021)
4-185320805-G-C		not specified	Uncertain significance (Nov 01, 2022)
4-185323576-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-185323589-T-C		not specified	Uncertain significance (Sep 16, 2021)
4-185332625-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-185332650-A-G		not specified	Uncertain significance (Mar 07, 2024)
4-185339415-G-A		not specified	Uncertain significance (Mar 01, 2024)
4-185339424-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-185339508-G-A		not specified	Uncertain significance (Mar 01, 2023)
4-185342042-G-A		not specified	Uncertain significance (Nov 10, 2022)
4-185342064-C-G		not specified	Uncertain significance (Feb 09, 2022)
4-185346573-C-G		not specified	Uncertain significance (Dec 15, 2023)
4-185351532-G-A		not specified	Uncertain significance (May 18, 2022)
4-185351587-G-A		not specified	Uncertain significance (Oct 17, 2023)
4-185353569-A-G		not specified	Uncertain significance (Nov 22, 2023)
4-185353575-A-T		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX25	protein_coding	protein_coding	ENST00000504273	18	165949

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000818	1.00	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.416	415	440	0.944	0.0000223	5595
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000415
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.000269	0.000261
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0914
• hipred: N
• hipred_score: 0.368
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx25
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• 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
• Cellular component: cellular_component;endosome membrane;intracellular membrane-bounded organelle
• Molecular function: molecular_function;type I transforming growth factor beta receptor binding;phosphatidylinositol binding