SPOUT1

SPOUT domain containing methyltransferase 1, the group of SPOUT methyltransferase domain containing

Basic information

Region (hg38): 9:128819651-128829794

Previous symbols: [ "C9orf114" ]

Links

ENSG00000198917 ∙ NCBI:51490 ∙ OMIM:617614 ∙ HGNC:26933 ∙ Uniprot:Q5T280 ∙ 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 SPOUT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPOUT1 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	4	5
missense		7	6		4	17
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding			11		4	15
Total	0	7	18	1	12

Variants in SPOUT1

This is a list of pathogenic ClinVar variants found in the SPOUT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128820748-C-T		not specified	Uncertain significance (Sep 20, 2023)
9-128820773-T-C		not specified	Uncertain significance (Jan 23, 2023)
9-128820787-C-T		not specified	Uncertain significance (Jan 25, 2023)
9-128820814-G-A		not specified	Uncertain significance (Jan 26, 2023)
9-128822364-G-C		not specified	Uncertain significance (Sep 22, 2023)
9-128822370-C-T			Benign (Jun 27, 2018)
9-128822444-A-G		not specified	Uncertain significance (Oct 03, 2022)
9-128822450-G-T			Benign (Jul 30, 2018)
9-128822453-C-T			Benign (Jul 30, 2018)
9-128822473-C-T		not specified	Uncertain significance (Jan 17, 2024)
9-128822500-C-T		not specified	Uncertain significance (Sep 28, 2022)
9-128822501-G-A		not specified	Uncertain significance (Jan 16, 2024)
9-128822537-C-T		not specified	Uncertain significance (Nov 01, 2022)
9-128822570-G-A		not specified	Uncertain significance (Jun 27, 2022)
9-128822601-CAGTA-C		not specified	Benign (Jun 17, 2015)
9-128822790-A-G		SPOUT1-related disorder	Benign (Oct 16, 2019)
9-128822807-G-C		SPOUT1-related disorder	Benign (Jun 11, 2019)
9-128822826-A-G		not specified	Uncertain significance (Nov 05, 2021)
9-128823739-G-A		SPOUT1-related disorder	Likely benign (Jun 13, 2019)
9-128823751-G-A		Neurodevelopmental disorder • SPOUT1-associated neurodevelopmental disorder	Conflicting classifications of pathogenicity (Jul 24, 2024)
9-128823755-G-A		Neurodevelopmental disorder	Likely pathogenic (May 20, 2024)
9-128823764-G-A		not specified	Uncertain significance (Jun 10, 2024)
9-128823781-C-G		not specified	Uncertain significance (Aug 12, 2021)
9-128823792-G-T		not specified	Uncertain significance (Jun 10, 2024)
9-128823793-T-C		Neurodevelopmental disorder	Likely pathogenic (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPOUT1	protein_coding	protein_coding	ENST00000361256	12	10171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.13e-9	0.804	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	177	233	0.759	0.0000149	2385
Missense in Polyphen		56	74.249	0.75422		720
Synonymous	0.240	94	97.0	0.969	0.00000610	739
Loss of Function	1.56	17	25.5	0.667	0.00000139	263

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000192	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000291	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for association of the centrosomes with the poles of the bipolar mitotic spindle during metaphase (PubMed:20813266, PubMed:25657325). Also involved in chromosome alignment (PubMed:20813266). May promote centrosome maturation probably by recruiting A-kinase anchor protein AKAP9 to centrosomes in early mitosis (PubMed:25657325). Binds specifically to miRNA MIR145 hairpin, regulates MIR145 expression at a postranscriptional level (PubMed:28431233). {ECO:0000269|PubMed:20813266, ECO:0000269|PubMed:25657325, ECO:0000269|PubMed:28431233}.

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.488
• ghis: 0.502

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Spout1
• 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); reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: cell cycle;posttranscriptional regulation of gene expression;methylation;production of miRNAs involved in gene silencing by miRNA;cell division;maintenance of centrosome location
• Cellular component: kinetochore;condensed chromosome kinetochore;cytoplasm;spindle pole centrosome;mitotic spindle
• Molecular function: RNA binding;protein binding;methyltransferase activity;miRNA binding