SPOUT1

protein-coding

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

Gene summary

Enables S-adenosyl-L-methionine binding activity; miRNA binding activity; and rRNA (uridine-N3-)-methyltransferase activity. Involved in maintenance of centrosome location; miRNA processing; and rRNA base methylation. Acts upstream of with a positive effect on post-transcriptional regulation of gene expression. Located in kinetochore; mitotic spindle; and spindle pole centrosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C9orf114

MANE transcript

NM_016390.4

Inheritance

ClinVar variants

P:8U:23B:7

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr9:128,819,651-128,829,794

External References & Databases

Ensembl (ENSG00000198917)

Transcript & Mutation Effects

hg38 • Region Span ~10.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPOUT1 variants in ClinVar

8 Conditions Cataloged

Neurodevelopmental disorderTotal: 10

SPOUT1-related disorderTotal: 10

not specifiedTotal: 7

not providedTotal: 6

Neurodevelopmental disorder with poor growth, seizures, and brain abnormalitiesTotal: 6

SPOUT1 Associated Development delay Microcephaly Seizures Short statureTotal: 2

Undetermined early-onset epileptic encephalopathyTotal: 1

SPOUT1-associated neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016390.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar	2 clinvar	7
missense		8 clinvar	13 clinvar	1 clinvar	1 clinvar	23
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	8	23	4	3	38

Highest pathogenic variant AF is 0.00018772863

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016390.4	RefSeq	NP_057474.2	12	MANE Select
ENST00000361256.10	Ensembl	ENSP00000354812.5	12	MANE Select
ENST00000467582.1	Ensembl	ENSP00000473640.1	3	Standard
ENST00000853913.1	Ensembl	ENSP00000523972.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell cycle
posttranscriptional regulation of gene expression
methylation
production of miRNAs involved in gene silencing by miRNA
cell division

Molecular Function

RNA binding
protein binding
methyltransferase activity
miRNA binding

Cellular Component

kinetochore
condensed chromosome kinetochore
cytoplasm
spindle pole centrosome
mitotic spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361256
Coding exons: 12
Length: 10171
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125748
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.31	177	233	0.759	0.0000149	2385
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00029	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): E