SNX22

sorting nexin 22, the group of Sorting nexins

Basic information

Region (hg38): 15:64151715-64157481

Links

ENSG00000157734 ∙ NCBI:79856 ∙ ∙ HGNC:16315 ∙ Uniprot:Q96L94 ∙ 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 SNX22 gene.

• Osteogenesis imperfecta type 9 (2 variants)
• not provided (2 variants)
• Osteogenesis imperfecta (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX22 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	3		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2	4	26	12	4	48
Total	2	4	35	15	4

Highest pathogenic variant AF is 0.0000197

Variants in SNX22

This is a list of pathogenic ClinVar variants found in the SNX22 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-64151803-G-A		not specified	Uncertain significance (Dec 10, 2024)
15-64151822-C-T		not specified	Uncertain significance (Aug 04, 2023)
15-64151825-G-C		not specified	Uncertain significance (Jul 15, 2021)
15-64151836-G-A		not specified	Uncertain significance (Jan 31, 2024)
15-64152319-A-G		not specified	Uncertain significance (Jul 14, 2023)
15-64152672-C-T		not specified	Uncertain significance (Jan 26, 2022)
15-64153252-T-G		not specified	Uncertain significance (Feb 17, 2022)
15-64153263-C-A		not specified	Uncertain significance (Sep 13, 2023)
15-64153302-C-G		not specified	Uncertain significance (Nov 09, 2024)
15-64153333-A-G		not specified	Likely benign (Jan 26, 2022)
15-64153672-C-G		not specified	Uncertain significance (Aug 02, 2021)
15-64153674-G-A		not specified	Likely benign (Jan 22, 2024)
15-64153952-G-A		not specified	Uncertain significance (Jul 12, 2023)
15-64154390-C-T		not specified	Likely benign (Sep 25, 2023)
15-64154444-T-G		not specified	Uncertain significance (Sep 25, 2024)
15-64154455-A-G		not specified	Uncertain significance (May 22, 2024)
15-64154504-C-T		not specified	Uncertain significance (Sep 02, 2024)
15-64155818-A-AT		Osteogenesis Imperfecta, Recessive	Benign/Likely benign (Aug 11, 2019)
15-64155820-T-TA		Osteogenesis Imperfecta, Recessive	Benign (Aug 20, 2019)
15-64155820-T-TAA		Osteogenesis Imperfecta, Recessive	Uncertain significance (Jun 14, 2016)
15-64155833-A-C		Osteogenesis imperfecta type 9	Uncertain significance (Jan 13, 2018)
15-64155833-A-AC		Osteogenesis Imperfecta, Recessive	Uncertain significance (Jun 14, 2016)
15-64155869-G-A		Osteogenesis imperfecta type 9	Uncertain significance (Apr 06, 2018)
15-64155943-G-A		Osteogenesis imperfecta type 9	Uncertain significance (Jan 12, 2018)
15-64155958-C-G		Osteogenesis imperfecta type 9	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX22	protein_coding	protein_coding	ENST00000325881	7	5767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00476	0.890	125735	0	7	125742	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0190	101	100	1.01	0.00000499	1243
Missense in Polyphen		45	42.093	1.0691		516
Synonymous	-0.426	47	43.4	1.08	0.00000224	374
Loss of Function	1.38	5	9.61	0.520	4.11e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000879
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in several stages of intracellular trafficking (By similarity). Interacts with membranes containing phosphatidylinositol 3-phosphate (PtdIns(3P)). {ECO:0000250}.

Recessive Scores

• pRec: 0.0814

Intolerance Scores

• loftool: 0.400
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.207
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx22
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

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