SPNS1

SPNS lysolipid transporter 1, lysophospholipid, the group of Solute carrier family 63, sphingosine phosphate transporters

Basic information

Region (hg38): 16:28974221-28984548

Links

ENSG00000169682 ∙ NCBI:83985 ∙ OMIM:612583 ∙ HGNC:30621 ∙ Uniprot:Q9H2V7 ∙ 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 SPNS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPNS1 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				2	1	3
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	4	1

Variants in SPNS1

This is a list of pathogenic ClinVar variants found in the SPNS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28975252-C-T		not specified	Uncertain significance (Mar 20, 2024)
16-28975263-G-A		not specified	Uncertain significance (Mar 15, 2024)
16-28975265-G-T		not specified	Likely benign (Apr 06, 2024)
16-28975351-A-G		not specified	Uncertain significance (Oct 17, 2023)
16-28977975-G-T		not specified	Uncertain significance (Aug 13, 2021)
16-28978039-G-A		not specified	Likely benign (Feb 03, 2022)
16-28979444-G-C		not specified	Uncertain significance (Feb 14, 2023)
16-28981534-G-A		not specified	Uncertain significance (Aug 11, 2024)
16-28981548-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-28981909-T-A		not specified	Uncertain significance (May 11, 2022)
16-28981966-T-C		not specified	Uncertain significance (Jan 18, 2022)
16-28981996-G-A		not specified	Uncertain significance (Sep 10, 2024)
16-28982038-C-T		not specified	Uncertain significance (May 07, 2024)
16-28982371-C-A			Likely benign (Dec 01, 2022)
16-28982386-C-T			Likely benign (Dec 01, 2022)
16-28982402-G-A		not specified	Uncertain significance (Aug 01, 2024)
16-28982437-C-G		not specified	Uncertain significance (Oct 01, 2024)
16-28982450-G-A		not specified	Uncertain significance (May 10, 2022)
16-28982908-G-T		not specified	Uncertain significance (Feb 28, 2024)
16-28982911-G-A		not specified	Uncertain significance (Dec 13, 2022)
16-28983283-T-C		not specified	Uncertain significance (Nov 10, 2024)
16-28983805-G-A		not specified	Uncertain significance (Sep 20, 2024)
16-28983827-G-T		not specified	Uncertain significance (Nov 08, 2022)
16-28983858-A-G		not specified	Uncertain significance (Jun 28, 2024)
16-28983867-G-A		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPNS1	protein_coding	protein_coding	ENST00000311008	12	10328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0204	0.979	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	237	344	0.688	0.0000226	3318
Missense in Polyphen		62	125.75	0.49303		1269
Synonymous	0.797	137	149	0.917	0.00000962	1210
Loss of Function	2.97	7	22.1	0.317	0.00000103	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000481	0.0000462
European (Non-Finnish)	0.0000447	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death. {ECO:0000250, ECO:0000269|PubMed:12815463}.

Recessive Scores

• pRec: 0.300

Intolerance Scores

• loftool: 0.579
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.747
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spns1
• 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: spns1
• Affected structure: cell
• Phenotype tag: abnormal
• Phenotype quality: accumulation

Gene ontology

• Biological process: lipid transport;transmembrane transport
• Cellular component: mitochondrial inner membrane;lysosomal membrane;integral component of membrane
• Molecular function: protein binding