SNX24

sorting nexin 24, the group of Sorting nexins

Basic information

Region (hg38): 5:122843438-123029354

Links

ENSG00000064652 ∙ NCBI:28966 ∙ ∙ HGNC:21533 ∙ Uniprot:Q9Y343 ∙ 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 SNX24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX24 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in SNX24

This is a list of pathogenic ClinVar variants found in the SNX24 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-122845671-G-A		not specified	Uncertain significance (Nov 21, 2022)
5-122936801-A-T		not specified	Uncertain significance (Dec 19, 2022)
5-122936816-A-G		not specified	Uncertain significance (Mar 15, 2024)
5-122946116-A-G		not specified	Uncertain significance (Feb 02, 2024)
5-122999921-T-G		not specified	Uncertain significance (Apr 13, 2022)
5-122999956-T-G		not specified	Uncertain significance (May 24, 2023)
5-122999969-C-G		not specified	Uncertain significance (Jul 09, 2021)
5-123001955-G-C		not specified	Uncertain significance (Apr 07, 2023)
5-123001978-A-T		not specified	Uncertain significance (May 14, 2024)
5-123001992-C-T		not specified	Uncertain significance (Mar 27, 2023)
5-123007726-T-A		not specified	Uncertain significance (Apr 07, 2023)
5-123023880-A-C		not specified	Uncertain significance (Dec 14, 2023)
5-123023886-C-T		not specified	Uncertain significance (Oct 03, 2022)
5-123023946-T-C		not specified	Likely benign (Jul 14, 2021)
5-123023959-G-T		not specified	Uncertain significance (Dec 20, 2021)
5-123025905-C-T		not specified	Uncertain significance (Oct 27, 2022)
5-123025924-G-C		not specified	Uncertain significance (Jan 19, 2024)
5-123028777-C-T		not specified	Uncertain significance (May 24, 2024)
5-123029312-G-A		not specified	Uncertain significance (Apr 07, 2023)
5-123029340-T-C		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX24	protein_coding	protein_coding	ENST00000261369	7	185916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000955	0.565	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.346	74	82.9	0.893	0.00000386	1088
Missense in Polyphen		25	33.534	0.74552		413
Synonymous	0.709	25	29.9	0.835	0.00000137	304
Loss of Function	0.769	9	11.9	0.759	6.80e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000129
Ashkenazi Jewish	0.000428	0.000198
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000207	0.000176
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000660	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.690
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.466
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx24

Gene ontology

• Biological process: protein transport
• Cellular component: cytoplasmic vesicle membrane
• Molecular function: phosphatidylinositol-5-phosphate binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-4-phosphate binding