SNX4

sorting nexin 4, the group of PX-BAR domain containing|Sorting nexins|Autophagy related

Basic information

Region (hg38): 3:125446650-125520202

Links

ENSG00000114520 ∙ NCBI:8723 ∙ OMIM:605931 ∙ HGNC:11175 ∙ Uniprot:O95219 ∙ 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 SNX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX4 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						0
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	0

Variants in SNX4

This is a list of pathogenic ClinVar variants found in the SNX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-125447788-G-C		not specified	Uncertain significance (Jun 06, 2023)
3-125451343-T-C		not specified	Uncertain significance (Nov 15, 2024)
3-125451363-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-125451397-C-T		not specified	Uncertain significance (Dec 14, 2023)
3-125451402-G-A		not specified	Uncertain significance (Feb 13, 2024)
3-125453900-G-A		not specified	Uncertain significance (May 26, 2024)
3-125453921-G-A		not specified	Uncertain significance (Jan 19, 2025)
3-125457312-T-C		not specified	Uncertain significance (Feb 19, 2025)
3-125457315-G-C		not specified	Uncertain significance (Jan 20, 2025)
3-125460780-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-125460837-A-C		not specified	Uncertain significance (Jan 22, 2025)
3-125469460-A-G		not specified	Uncertain significance (Nov 23, 2024)
3-125469485-C-T		not specified	Uncertain significance (Mar 31, 2024)
3-125476734-C-T		not specified	Uncertain significance (Jan 28, 2025)
3-125476743-C-T		not specified	Uncertain significance (May 12, 2024)
3-125480300-G-A		not specified	Uncertain significance (Jul 27, 2022)
3-125480308-T-C		not specified	Uncertain significance (Dec 28, 2023)
3-125489412-C-A		not specified	Uncertain significance (Dec 22, 2023)
3-125497864-T-G		not specified	Uncertain significance (Nov 14, 2023)
3-125497938-C-G		not specified	Uncertain significance (Jan 14, 2025)
3-125498060-C-T		not specified	Uncertain significance (Nov 25, 2024)
3-125498118-T-C		not specified	Uncertain significance (Oct 30, 2023)
3-125498148-A-C		not specified	Uncertain significance (Jan 23, 2023)
3-125498150-A-G		not specified	Uncertain significance (Dec 12, 2024)
3-125498175-C-T		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX4	protein_coding	protein_coding	ENST00000251775	14	73547

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.68e-8	0.992	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.887	190	228	0.835	0.0000111	2941
Missense in Polyphen		39	49.148	0.79352		610
Synonymous	-0.827	85	75.8	1.12	0.00000355	782
Loss of Function	2.45	17	31.9	0.533	0.00000190	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000272
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000271	0.000264
Middle Eastern	0.00	0.00
South Asian	0.000263	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. Plays a role in recycling endocytosed transferrin receptor and prevent its degradation. {ECO:0000269|PubMed:17994011}.
• Pathway: Endocytosis - Homo sapiens (human);TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.814
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.380
• hipred: Y
• hipred_score: 0.718
• ghis: 0.696

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.641

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx4

Gene ontology

• Biological process: protein transport;endocytic recycling;positive regulation of histamine secretion by mast cell
• Cellular component: cytoplasm;cytoplasmic dynein complex;plasma membrane;membrane;SNARE complex;early endosome membrane;protein-containing complex
• Molecular function: epidermal growth factor receptor binding;insulin receptor binding;protein binding;phosphatidylinositol binding;transferrin receptor binding;leptin receptor binding