SNX7

sorting nexin 7, the group of PX-BAR domain containing|Sorting nexins

Basic information

Region (hg38): 1:98661700-98760500

Links

ENSG00000162627 ∙ NCBI:51375 ∙ OMIM:614904 ∙ HGNC:14971 ∙ Uniprot:Q9UNH6 ∙ 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 SNX7 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX7 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			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	1

Variants in SNX7

This is a list of pathogenic ClinVar variants found in the SNX7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-98661762-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-98661769-C-T		not specified	Uncertain significance (Jul 12, 2023)
1-98661778-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-98661786-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-98661786-G-C		not specified	Uncertain significance (Mar 07, 2023)
1-98661786-G-T		not specified	Uncertain significance (Nov 29, 2021)
1-98661814-G-C		not specified	Uncertain significance (Jun 24, 2022)
1-98661820-C-T		not specified	Uncertain significance (May 16, 2022)
1-98661847-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-98684924-A-C		not specified	Uncertain significance (Mar 06, 2023)
1-98684945-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-98684949-T-C		not specified	Uncertain significance (Jun 28, 2022)
1-98685051-A-G		not specified	Uncertain significance (Feb 03, 2022)
1-98685060-T-C		not specified	Uncertain significance (May 23, 2023)
1-98691130-A-T		not specified	Uncertain significance (Nov 08, 2022)
1-98691172-C-T		not specified	Uncertain significance (Aug 31, 2022)
1-98691575-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-98691580-A-C		not specified	Uncertain significance (Dec 28, 2023)
1-98695543-G-C		not specified	Uncertain significance (Aug 04, 2022)
1-98695545-C-G		not specified	Uncertain significance (Dec 21, 2023)
1-98695628-C-A			Benign (Mar 06, 2018)
1-98698839-G-A		not specified	Uncertain significance (Jan 17, 2023)
1-98698867-G-A		not specified	Uncertain significance (Nov 17, 2023)
1-98698871-T-C		not specified	Uncertain significance (Sep 14, 2022)
1-98698882-G-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX7	protein_coding	protein_coding	ENST00000306121	9	98821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000373	0.955	125714	0	32	125746	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.369	190	205	0.927	0.0000102	2989
Missense in Polyphen		50	68.784	0.72691		1043
Synonymous	0.138	67	68.5	0.979	0.00000361	796
Loss of Function	1.83	10	18.5	0.540	8.75e-7	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000204	0.000204
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000987	0.0000924
European (Non-Finnish)	0.000156	0.000149
Middle Eastern	0.000165	0.000163
South Asian	0.0000662	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking.

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.790
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.544
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.819

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx7

Zebrafish Information Network

• Gene name: snx7
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: protein transport
• Cellular component: cytoplasmic vesicle membrane
• Molecular function: protein binding;phosphatidylinositol binding