SNX31

sorting nexin 31, the group of Sorting nexins

Basic information

Region (hg38): 8:100572889-100663415

Links

ENSG00000174226 ∙ NCBI:169166 ∙ OMIM:619839 ∙ HGNC:28605 ∙ Uniprot:Q8N9S9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNX31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX31 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			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in SNX31

This is a list of pathogenic ClinVar variants found in the SNX31 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-100573884-A-G		not specified	Uncertain significance (May 06, 2024)
8-100573926-C-T		not specified	Uncertain significance (Nov 03, 2023)
8-100573942-A-T		not specified	Uncertain significance (May 05, 2023)
8-100573953-T-C		not specified	Uncertain significance (Aug 30, 2022)
8-100577062-G-A		not specified	Uncertain significance (Feb 26, 2024)
8-100584133-A-G		not specified	Uncertain significance (Apr 09, 2024)
8-100588874-T-C		not specified	Uncertain significance (Feb 17, 2024)
8-100596690-C-A		not specified	Uncertain significance (Jun 07, 2024)
8-100596695-T-G		not specified	Uncertain significance (Mar 23, 2022)
8-100596742-A-G		not specified	Uncertain significance (Dec 08, 2023)
8-100596786-A-C		not specified	Uncertain significance (Oct 06, 2022)
8-100596822-C-A		not specified	Uncertain significance (Sep 17, 2021)
8-100600389-T-C		not specified	Uncertain significance (Jan 26, 2022)
8-100608549-G-A		not specified	Uncertain significance (Sep 25, 2023)
8-100612078-T-C		not specified	Uncertain significance (Apr 29, 2024)
8-100613019-A-G		not specified	Uncertain significance (Feb 28, 2023)
8-100613046-C-T		not specified	Uncertain significance (May 22, 2023)
8-100617642-T-C		not specified	Uncertain significance (Jan 02, 2024)
8-100617650-T-C		not specified	Uncertain significance (Dec 01, 2022)
8-100617664-T-C		not specified	Uncertain significance (Sep 25, 2023)
8-100630334-G-A		not specified	Likely benign (Aug 16, 2022)
8-100630353-C-T		not specified	Likely benign (Apr 27, 2022)
8-100630374-C-A		not specified	Uncertain significance (Sep 17, 2021)
8-100630379-G-C		not specified	Uncertain significance (Feb 16, 2023)
8-100635948-T-G		not specified	Uncertain significance (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX31	protein_coding	protein_coding	ENST00000311812	14	90528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.67e-13	0.286	124103	46	1599	125748	0.00656

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0561	234	236	0.990	0.0000120	2898
Missense in Polyphen		63	61.18	1.0297		784
Synonymous	-0.319	94	90.1	1.04	0.00000493	774
Loss of Function	1.15	23	29.7	0.773	0.00000141	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0735	0.0724
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.0150	0.0150
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000768	0.000765
Middle Eastern	0.0150	0.0150
South Asian	0.000956	0.000948
Other	0.00343	0.00343

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in protein trafficking. {ECO:0000250}.

Recessive Scores

• pRec: 0.0614

Intolerance Scores

• loftool: 0.953
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.0546
• hipred: N
• hipred_score: 0.182

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx31
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: intracellular protein transport;retrograde transport, endosome to plasma membrane
• Cellular component: early endosome;protein-containing complex
• Molecular function: protein binding;phosphatidylinositol binding