SPNS3

SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative), the group of Solute carrier family 63, sphingosine phosphate transporters

Basic information

Region (hg38): 17:4433940-4488208

Links

ENSG00000182557 ∙ NCBI:201305 ∙ OMIM:611701 ∙ HGNC:28433 ∙ Uniprot:Q6ZMD2 ∙ 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 SPNS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPNS3 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				1		1
missense			43	8		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	9	0

Variants in SPNS3

This is a list of pathogenic ClinVar variants found in the SPNS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4434062-T-G		not specified	Likely benign (Nov 30, 2022)
17-4434065-C-T		not specified	Uncertain significance (Sep 01, 2024)
17-4434106-G-A		not specified	Uncertain significance (Feb 06, 2024)
17-4434118-C-T		not specified	Uncertain significance (Sep 10, 2024)
17-4434131-A-C		not specified	Uncertain significance (Mar 16, 2024)
17-4434145-A-G		not specified	Uncertain significance (Feb 12, 2024)
17-4439705-G-A		not specified	Uncertain significance (Dec 04, 2024)
17-4445037-G-A		not specified	Likely benign (Nov 10, 2022)
17-4445059-C-T		not specified	Uncertain significance (May 05, 2022)
17-4445085-C-G		not specified	Uncertain significance (Nov 21, 2024)
17-4445094-C-T			Likely benign (Dec 01, 2022)
17-4445142-C-T		not specified	Uncertain significance (Dec 16, 2023)
17-4445167-G-A		not specified	Likely benign (Jul 20, 2021)
17-4446062-C-A		not specified	Uncertain significance (Sep 22, 2022)
17-4446072-C-T		not specified	Uncertain significance (Jun 09, 2022)
17-4446076-G-T		not specified	Uncertain significance (Apr 04, 2023)
17-4446115-C-T		not specified	Uncertain significance (Apr 12, 2024)
17-4446123-G-A		not specified	Uncertain significance (May 27, 2022)
17-4446132-G-A		not specified	Uncertain significance (Aug 21, 2023)
17-4446141-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-4446151-A-G		not specified	Uncertain significance (Jun 03, 2024)
17-4446153-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-4446154-G-A		not specified	Uncertain significance (Aug 21, 2024)
17-4446159-C-T		not specified	Uncertain significance (Jul 06, 2021)
17-4446160-G-A		not specified	Uncertain significance (May 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPNS3	protein_coding	protein_coding	ENST00000355530	12	54521

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-12	0.109	125012	2	734	125748	0.00293

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.338	301	318	0.947	0.0000203	3207
Missense in Polyphen		84	90.63	0.92685		931
Synonymous	-2.29	178	143	1.24	0.0000100	1120
Loss of Function	0.621	20	23.2	0.861	0.00000108	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00261	0.00260
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00276	0.00254
European (Non-Finnish)	0.00499	0.00498
Middle Eastern	0.000272	0.000272
South Asian	0.00156	0.00144
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sphingolipid transporter. {ECO:0000250}.

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.789
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.32

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.170
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spns3

Gene ontology

• Biological process: lipid transport;transmembrane transport
• Cellular component: integral component of membrane