SPX

spexin hormone

Basic information

Region (hg38): 12:21526296-21541249

Previous symbols: [ "C12orf39" ]

Links

ENSG00000134548 ∙ NCBI:80763 ∙ OMIM:619246 ∙ HGNC:28139 ∙ Uniprot:Q9BT56 ∙ 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 SPX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPX 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in SPX

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

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

Position	Type	Phenotype	Significance	ClinVar
12-21526911-C-T		not specified	Likely benign (Dec 19, 2023)
12-21526941-T-C		not specified	Uncertain significance (Mar 15, 2023)
12-21526958-G-C		not specified	Uncertain significance (Mar 25, 2022)
12-21527142-T-C		not specified	Uncertain significance (Jan 30, 2024)
12-21527759-A-G		not specified	Uncertain significance (May 06, 2022)
12-21527765-G-A		not specified	Uncertain significance (Oct 04, 2022)
12-21527777-C-T		not specified	Uncertain significance (Mar 19, 2024)
12-21529007-G-A		not specified	Uncertain significance (Feb 10, 2022)
12-21529033-A-G		not specified	Uncertain significance (Oct 17, 2023)
12-21529046-C-A		not specified	Uncertain significance (Dec 30, 2023)
12-21531137-A-C		not specified	Likely benign (Nov 22, 2023)
12-21536211-GTTTA-G		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jun 14, 2016)
12-21536270-G-A		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 13, 2018)
12-21536300-C-T		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 13, 2018)
12-21536322-AC-A		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jun 14, 2016)
12-21536386-AT-A		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jun 14, 2016)
12-21536409-C-T		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 13, 2018)
12-21536434-T-C		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 12, 2018)
12-21536486-A-G		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 13, 2018)
12-21536496-T-A		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 12, 2018)
12-21536516-T-TA		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Likely benign (Jun 14, 2016)
12-21536546-T-C		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 13, 2018)
12-21536548-A-C		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 13, 2018)
12-21536595-G-A		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Uncertain significance (Jan 12, 2018)
12-21536664-C-A		Glycogen storage disorder due to hepatic glycogen synthase deficiency	Benign (Apr 27, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPX	protein_coding	protein_coding	ENST00000256969	6	11071

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000110	0.613	125719	0	28	125747	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.115	63	60.5	1.04	0.00000294	737
Missense in Polyphen		17	16.839	1.0096		199
Synonymous	1.74	14	25.1	0.558	0.00000136	233
Loss of Function	0.715	7	9.36	0.748	6.42e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000967	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a central modulator of cardiovascular and renal function and nociception. Plays also a role in energy metabolism and storage. Inhibits adrenocortical cell proliferation with minor stimulation on corticosteroid release (By similarity). {ECO:0000250}.; FUNCTION: Spexin-2: Intracerebroventricular administration of the peptide induces a decrease in heart rate, but no change in arterial pressure, and an increase in urine flow rate. Intraventricular administration of the peptide induces antinociceptive activity (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.180
• ghis: 0.536

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spx

Gene ontology

• Biological process: positive regulation of systemic arterial blood pressure;negative regulation of heart rate;regulation of signaling receptor activity;negative regulation of appetite;negative regulation of renal sodium excretion;long-chain fatty acid import;regulation of sensory perception of pain;positive regulation of gastro-intestinal system smooth muscle contraction
• Cellular component: extracellular space;cytoplasm;transport vesicle;dense core granule
• Molecular function: neuropeptide hormone activity