SNX32

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

Basic information

Region (hg38): 11:65833833-65856896

Previous symbols: [ "SNX6B" ]

Links

ENSG00000172803 ∙ NCBI:254122 ∙ ∙ HGNC:26423 ∙ Uniprot:Q86XE0 ∙ 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 SNX32 gene.

• Inborn genetic diseases (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX32 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in SNX32

This is a list of pathogenic ClinVar variants found in the SNX32 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65849545-G-C		not specified	Uncertain significance (Dec 18, 2023)
11-65849924-G-A		not specified	Uncertain significance (Dec 16, 2023)
11-65850001-G-A		not specified	Uncertain significance (Jan 26, 2022)
11-65850235-G-C		not specified	Uncertain significance (Sep 17, 2021)
11-65850240-G-A		not specified	Uncertain significance (Jul 06, 2022)
11-65850456-A-G		not specified	Uncertain significance (May 05, 2023)
11-65850466-T-C		not specified	Uncertain significance (Feb 15, 2023)
11-65850471-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-65850501-C-T		not specified	Uncertain significance (May 25, 2022)
11-65850514-G-A		not specified	Likely benign (May 10, 2023)
11-65850761-G-A		not specified	Uncertain significance (Oct 03, 2023)
11-65850791-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-65850836-C-T		not specified	Uncertain significance (May 17, 2023)
11-65850839-G-A		not specified	Uncertain significance (Nov 06, 2023)
11-65850842-T-C		not specified	Uncertain significance (Nov 14, 2023)
11-65850850-C-A		not specified	Uncertain significance (Feb 15, 2023)
11-65851086-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-65851097-G-A		not specified	Uncertain significance (Nov 04, 2022)
11-65851110-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-65851373-T-G		not specified	Uncertain significance (Jan 04, 2024)
11-65851392-C-A		not specified	Uncertain significance (Feb 06, 2023)
11-65851675-T-C		not specified	Uncertain significance (May 31, 2023)
11-65852471-G-A		not specified	Uncertain significance (Mar 04, 2024)
11-65852532-G-A		not specified	Uncertain significance (Aug 30, 2022)
11-65852642-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX32	protein_coding	protein_coding	ENST00000308342	13	23256

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.83e-18	0.00340	125552	1	195	125748	0.000780

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.259	275	263	1.04	0.0000185	2619
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00176	0.00175
Ashkenazi Jewish	0.00110	0.00109
East Asian	0.00171	0.00169
Finnish	0.000288	0.000277
European (Non-Finnish)	0.000629	0.000624
Middle Eastern	0.00171	0.00169
South Asian	0.00109	0.00108
Other	0.00114	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking. {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.920
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.170
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx32

Gene ontology

• Biological process: protein transport;regulation of macroautophagy
• Molecular function: protein binding;phosphatidylinositol binding