SNX14

sorting nexin 14, the group of Sorting nexins

Basic information

Region (hg38): 6:85504776-85594156

Links

ENSG00000135317

∙ NCBI:57231 ∙ OMIM:616105 ∙ HGNC:14977 ∙ Uniprot:Q9Y5W7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

autosomal recessive spinocerebellar ataxia 20 (Strong), mode of inheritance: AR
autosomal recessive spinocerebellar ataxia 20 (Supportive), mode of inheritance: AR
autosomal recessive spinocerebellar ataxia 20 (Strong), mode of inheritance: AR
autosomal recessive spinocerebellar ataxia 20 (Strong), mode of inheritance: AR
autosomal recessive spinocerebellar ataxia 20 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive 20	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	24501761; 25439728; 25848753

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNX14 gene.

not_provided (201 variants)
Inborn_genetic_diseases (92 variants)
Autosomal_recessive_spinocerebellar_ataxia_20 (44 variants)
SNX14-related_disorder (15 variants)
Neurodevelopmental_disorder (2 variants)
not_specified (2 variants)
Cerebellar_ataxia (1 variants)
Spinocerebellar_atrophy (1 variants)
Seizure (1 variants)
Global_developmental_delay (1 variants)
Abnormal_brain_morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX14 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153816.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	38 clinvar	1 clinvar	42
missense	1 clinvar		132 clinvar	4 clinvar	1 clinvar	138
nonsense	6 clinvar	7 clinvar				13
start loss						0
frameshift	7 clinvar	7 clinvar				14
splice donor/acceptor (+/-2bp)	3 clinvar	12 clinvar				15
Total	17	26	135	42	2

Highest pathogenic variant AF is 0.0000477869

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX14	protein_coding	protein_coding	ENST00000314673	29	88661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.07e-17	0.982	125650	0	98	125748	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	350	462	0.758	0.0000218	6215
Missense in Polyphen		87	141.32	0.61564		1963
Synonymous	-0.719	169	158	1.07	0.00000731	1692
Loss of Function	2.61	35	56.1	0.624	0.00000270	748

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000525	0.000516
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00122	0.00114
Finnish	0.000144	0.000139
European (Non-Finnish)	0.000437	0.000422
Middle Eastern	0.00122	0.00114
South Asian	0.000405	0.000392
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a role in maintaining normal neuronal excitability and synaptic transmission. May be involved in several stages of intracellular trafficking (By similarity). Required for autophagosome clearance, possibly by mediating the fusion of lysosomes with autophagosomes (Probable). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2), a key component of late endosomes/lysosomes (PubMed:25848753). Does not bind phosphatidylinositol 3-phosphate (PtdIns(3P)) (PubMed:25848753, PubMed:25148684). {ECO:0000250|UniProtKB:Q8BHY8, ECO:0000269|PubMed:25148684, ECO:0000269|PubMed:25848753, ECO:0000305|PubMed:25848753}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

loftool: 0.964
rvis_EVS: -0.49
rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

pHI: 0.168
hipred: Y
hipred_score: 0.536
ghis: 0.619

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Snx14
Phenotype

Zebrafish Information Network

Gene name: snx14
Affected structure: neuron
Phenotype tag: abnormal
Phenotype quality: apoptotic

Gene ontology

Biological process: protein transport;autophagosome maturation
Cellular component: lysosome;lysosomal membrane;late endosome;integral component of membrane;dendrite;late endosome membrane
Molecular function: phosphatidylinositol-3,5-bisphosphate binding