SNU13

protein-coding

small nuclear ribonucleoprotein 13, the group of U3 small nucleolar ribonucleoprotein|U4/U6 small nuclear ribonucleoprotein

Gene summary

Originally named because of its sequence similarity to the Saccharomyces cerevisiae NHP2 (non-histone protein 2), this protein appears to be a highly conserved nuclear protein that is a component of the [U4/U6.U5] tri-snRNP. It binds to the 5' stem-loop of U4 snRNA. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

SSFA1
NHP2L1

MANE transcript

NM_001003796.2

Inheritance

—

ClinVar variants

U:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr22:41,673,933-41,690,504

External References & Databases

Ensembl (ENSG00000100138)

Transcript & Mutation Effects

hg38 • Region Span ~16.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNU13 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001003796.2. 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						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	2	0	0	2

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001003796.2	RefSeq	NP_001003796.1	3	MANE Select
ENST00000401959.6	Ensembl	ENSP00000383949.1	3	MANE Select
NM_005008.4	RefSeq	NP_004999.1	3	Standard
ENST00000215956.10	Ensembl	ENSP00000215956.5	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
snu13b	Danio rerio	Structure: somite development Quality: disrupted abnormal

Gene / Model

Organism

Observed Phenotype

snu13b

Danio rerio

Structure: somite development

Quality: disrupted

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
Spliceosome - Homo sapiens (human)
mRNA Processing
rRNA processing
Metabolism of RNA

Biological Process

mRNA splicing, via spliceosome
maturation of LSU-rRNA
box C/D snoRNP assembly
rRNA processing
single fertilization

Molecular Function

RNA binding
protein binding
snoRNA binding
U4 snRNA binding
U4atac snRNA binding

Cellular Component

dense fibrillar component
nucleus
nucleoplasm
U4atac snRNP
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401959
Coding exons: 3
Length: 16575
Individuals with no LoFs: 125416
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125417
p: 0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.20	21	74.6	0.282	0.00000425	818
Missense (PolyPhen)		0	15.445	0		211
Synonymous	-0.157	34	32.9	1.03	0.00000198	265
Loss of Function	1.98	0	4.57	0.00	1.91e-7	61

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:28781166). Binds to the 5'-stem-loop of U4 snRNA and thereby contributes to spliceosome assembly (PubMed:10545122, PubMed:17412961). The protein undergoes a conformational change upon RNA-binding (PubMed:17412961). {ECO:0000269|PubMed:10545122, ECO:0000269|PubMed:17412961, ECO:0000269|PubMed:28781166}.;

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 56.25

Essentials

Essential (gene trap): E