SNX12

sorting nexin 12, the group of Sorting nexins

Basic information

Region (hg38): X:71056331-71073426

Links

ENSG00000147164 ∙ NCBI:29934 ∙ OMIM:300883 ∙ HGNC:14976 ∙ Uniprot:Q9UMY4 ∙ 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 SNX12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX12 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in SNX12

This is a list of pathogenic ClinVar variants found in the SNX12 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-71061053-A-G		not specified	Uncertain significance (Sep 20, 2023)
X-71061086-C-T		not specified	Uncertain significance (Sep 27, 2021)
X-71062898-T-C		not specified	Uncertain significance (Apr 20, 2023)
X-71062910-G-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX12	protein_coding	protein_coding	ENST00000374274	4	9180

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.784	0.210	124351	0	1	124352	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	18	68.2	0.264	0.00000559	1057
Missense in Polyphen		8	33.284	0.24036		514
Synonymous	0.605	22	25.9	0.849	0.00000194	315
Loss of Function	2.09	0	5.08	0.00	3.88e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000123	0.00000889
Middle Eastern	0.00	0.00
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}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.593
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx12
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of gene expression;negative regulation of protein processing;protein transport;regulation of endocytosis;negative regulation of protein catabolic process;negative regulation of protein transport;negative regulation of early endosome to late endosome transport
• Cellular component: early endosome;membrane
• Molecular function: protein binding;enzyme binding;phosphatidylinositol binding