SNX30

sorting nexin family member 30, the group of Autophagy related|PX-BAR domain containing|Sorting nexins

Basic information

Region (hg38): 9:112750759-112881671

Links

ENSG00000148158 ∙ NCBI:401548 ∙ ∙ HGNC:23685 ∙ Uniprot:Q5VWJ9 ∙ 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 SNX30 gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX30 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	1

Variants in SNX30

This is a list of pathogenic ClinVar variants found in the SNX30 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-112751005-G-T		not specified	Likely benign (Apr 07, 2023)
9-112751059-A-G		not specified	Uncertain significance (Dec 19, 2023)
9-112751088-C-A		not specified	Uncertain significance (Jan 09, 2024)
9-112751116-C-G		not specified	Uncertain significance (Jan 09, 2024)
9-112804787-G-T		not specified	Uncertain significance (Aug 14, 2023)
9-112804867-A-G		not specified	Uncertain significance (Jun 22, 2023)
9-112804893-T-C		not specified	Uncertain significance (Jan 08, 2024)
9-112804899-A-G		not specified	Uncertain significance (Feb 17, 2022)
9-112817712-G-A		not specified	Uncertain significance (May 31, 2023)
9-112830768-T-C		not specified	Uncertain significance (Dec 06, 2022)
9-112830831-A-C		not specified	Uncertain significance (Jun 06, 2023)
9-112836223-G-A		not specified	Uncertain significance (Nov 21, 2022)
9-112836265-G-A		not specified	Uncertain significance (Jul 12, 2023)
9-112836355-C-T		not specified	Uncertain significance (Dec 07, 2023)
9-112836361-C-G		not specified	Uncertain significance (Jan 19, 2024)
9-112838548-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-112838568-T-C			Benign (Dec 23, 2021)
9-112838591-C-T		not specified	Uncertain significance (Jul 30, 2023)
9-112850937-C-T		not specified	Uncertain significance (Nov 15, 2023)
9-112864254-C-T		not specified	Uncertain significance (Sep 14, 2022)
9-112864259-G-A		not specified	Uncertain significance (Jul 11, 2023)
9-112864338-G-A		not specified	Uncertain significance (Oct 05, 2022)
9-112864350-G-A		not specified	Uncertain significance (Sep 01, 2021)
9-112864368-T-C		not specified	Uncertain significance (Apr 13, 2022)
9-112868829-C-A		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX30	protein_coding	protein_coding	ENST00000374232	9	130834

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.588	0.411	124786	0	7	124793	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.888	203	242	0.839	0.0000134	2848
Missense in Polyphen		98	108.48	0.90341		1211
Synonymous	1.38	77	94.0	0.819	0.00000548	847
Loss of Function	3.33	4	20.1	0.199	0.00000108	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000300	0.0000300
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.0790
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.654
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.324

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx30

Gene ontology

• Biological process: protein transport
• Molecular function: protein binding;phosphatidylinositol binding