SNX21

sorting nexin family member 21, the group of Tetratricopeptide repeat domain containing|Sorting nexins

Basic information

Region (hg38): 20:45833799-45843276

Previous symbols: [ "C20orf161" ]

Links

ENSG00000124104 ∙ NCBI:90203 ∙ OMIM:619200 ∙ HGNC:16154 ∙ Uniprot:Q969T3 ∙ 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 SNX21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX21 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			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	38	2	0

Variants in SNX21

This is a list of pathogenic ClinVar variants found in the SNX21 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45833923-C-G		not specified	Uncertain significance (Jun 06, 2023)
20-45834208-T-C		not specified	Uncertain significance (Jan 04, 2024)
20-45834210-G-T		not specified	Uncertain significance (Jun 17, 2022)
20-45834216-C-G		not specified	Uncertain significance (Oct 22, 2024)
20-45834234-C-T		not specified	Uncertain significance (Feb 13, 2025)
20-45834249-G-A		not specified	Uncertain significance (Apr 07, 2023)
20-45834265-A-G		not specified	Uncertain significance (Oct 01, 2024)
20-45834290-G-C		not specified	Uncertain significance (Jan 06, 2023)
20-45834353-C-A		not specified	Uncertain significance (Jan 19, 2024)
20-45834354-G-A		not specified	Uncertain significance (Feb 24, 2025)
20-45834383-C-G		not specified	Uncertain significance (Mar 05, 2025)
20-45834391-A-G		not specified	Uncertain significance (Jan 19, 2025)
20-45834413-G-C		not specified	Uncertain significance (Mar 05, 2025)
20-45835071-A-C		not specified	Uncertain significance (Dec 20, 2023)
20-45835088-T-A		not specified	Uncertain significance (May 15, 2024)
20-45835112-A-G		not specified	Uncertain significance (Aug 02, 2024)
20-45840650-C-T		not specified	Likely benign (Jul 05, 2023)
20-45840653-C-T		not specified	Likely benign (Mar 25, 2024)
20-45840654-G-A		not specified	Uncertain significance (Sep 30, 2024)
20-45840670-C-T		not specified	Uncertain significance (Sep 14, 2023)
20-45840679-G-A		not specified	Uncertain significance (Jul 26, 2024)
20-45840682-A-G		not specified	Uncertain significance (Nov 17, 2022)
20-45840699-C-T		not specified	Uncertain significance (Nov 30, 2022)
20-45840700-G-A		not specified	Uncertain significance (May 24, 2023)
20-45840709-C-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX21	protein_coding	protein_coding	ENST00000491381	4	9466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.32e-7	0.287	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.200	229	238	0.963	0.0000163	2352
Missense in Polyphen		80	76.164	1.0504		779
Synonymous	-0.332	105	101	1.04	0.00000568	826
Loss of Function	0.404	11	12.5	0.877	6.29e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000791	0.000747
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000162	0.000158
Middle Eastern	0.00	0.00
South Asian	0.000396	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to membranes enriched in phosphatidylinositol 3- phosphate (PtdIns(P3)) and phosphatidylinositol 4,5-bisphosphate. May be involved in several stages of intracellular trafficking. {ECO:0000250|UniProtKB:Q3UR97}.

Recessive Scores

• pRec: 0.0940

Intolerance Scores

• loftool: 0.398
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.219
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0416

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx21

Gene ontology

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