SPTSSA

serine palmitoyltransferase small subunit A

Basic information

Region (hg38): 14:34432788-34462240

Previous symbols: [ "C14orf147" ]

Links

ENSG00000165389

∙ NCBI:171546 ∙ OMIM:613540 ∙ HGNC:20361 ∙ Uniprot:Q969W0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

spastic paraplegia 90A, autosomal dominant (Strong), mode of inheritance: AD
spastic paraplegia 90B, autosomal recessive (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 90A, autosomal dominant; Spastic paraplegia 90B, autosomal recessive	AD/AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Neurologic	36718090

ClinVar

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

Variants pathogenicity by type

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

Variants in SPTSSA

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

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

Position	Phenotype	Significance	ClinVar
14-34435209-C-T	not specified	Uncertain significance (Mar 15, 2024)	3322534
14-34435244-TGG-T	Spastic paraplegia 90B, autosomal recessive	Pathogenic (Dec 07, 2023)	2505468
14-34435265-G-A	SPTSSA-related disorder • Spastic paraplegia 90A, autosomal dominant	Conflicting classifications of pathogenicity (Dec 07, 2023)	2505470
14-34462156-A-C	not specified	Uncertain significance (Oct 20, 2021)	2255922
14-34462156-A-T	not specified	Uncertain significance (Jan 04, 2022)	2269218
14-34462198-T-C	not specified	Uncertain significance (Aug 02, 2021)	2223447

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPTSSA	protein_coding	protein_coding	ENST00000298130	2	29568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.646	0.330	102420	0	1	102421	0.00000488

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.228	36	40.1	0.899	0.00000201	451
Missense in Polyphen		4	9.3588	0.42741		122
Synonymous	-0.970	23	17.8	1.29	0.00000101	135
Loss of Function	1.69	0	3.35	0.00	1.44e-7	36

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)	0.0000108	0.0000108
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Stimulates the activity of serine palmitoyltransferase (SPT). The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2- SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16- CoA as substrates, with a slight preference for C14-CoA. {ECO:0000269|PubMed:19416851}.;
Pathway: Metabolism of lipids;Metabolism;ceramide <i>de novo</i> biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool
rvis_EVS: -0.05
rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

pHI: 0.184
hipred: N
hipred_score: 0.400
ghis: 0.608

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: K
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sptssa
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); homeostasis/metabolism phenotype;

Gene ontology

Biological process: sphingolipid biosynthetic process;ceramide biosynthetic process
Cellular component: endoplasmic reticulum membrane;integral component of membrane;serine C-palmitoyltransferase complex
Molecular function: serine C-palmitoyltransferase activity;protein binding