SNRPE

protein-coding

small nuclear ribonucleoprotein polypeptide E, the group of Sm spliceosomal proteins

Gene summary

The protein encoded by this gene is a core component of U small nuclear ribonucleoproteins, which are key components of the pre-mRNA processing spliceosome. The encoded protein plays a role in the 3' end processing of histone transcripts. This protein is one of the targets in the autoimmune disease systemic lupus erythematosus, and mutations in this gene have been associated with hypotrichosis. Several pseudogenes of this gene have been identified. [provided by RefSeq, Jun 2016]

MANE transcript

NM_003094.4

Inheritance

ClinVar variants

P:5U:16B:1

Top phenotype

Hypotrichosis 11

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr1:203,861,599-203,871,152

External References & Databases

Ensembl (ENSG00000182004)

Transcript & Mutation Effects

hg38 • Region Span ~9.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hypotrichosis simplexSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018914

Submitter: Orphanet

hypotrichosis 11STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014027

Submitter: Labcorp Genetics (formerly Invitae)

hypotrichosis 11STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014027

Submitter: PanelApp Australia

hypotrichosis 11LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014027

Submitter: Ambry Genetics

hypotrichosis 11STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014027

Submitter: G2P

Clinical Genomic Database (CGD)

Hypotrichosis 11AD

Manifestation: Dermatologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 23246290

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SNRPE variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 6

Hypotrichosis 11Total: 5

SNRPE-related disorderTotal: 3

Long QT syndrome 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003094.4. 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				1 clinvar		1
missense	2 clinvar		9 clinvar			11
nonsense						0
start loss		1 clinvar	1 clinvar			2
frameshift		1 clinvar	2 clinvar			3
splice donor/acceptor (+/-2bp)	1 clinvar		4 clinvar			5
Total	3	2	16	1	0	22

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003094.4	RefSeq	NP_003085.1	5	MANE Select
ENST00000414487.7	Ensembl	ENSP00000400591.2	5	MANE Select
NM_001304464.2	RefSeq	NP_001291393.1	5	Standard
NM_001328637.2	RefSeq	NP_001315566.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
mRNA Processing
Gene expression (Transcription)
snRNP Assembly
RNA Polymerase II Transcription

Biological Process

spliceosomal complex assembly
spliceosomal snRNP assembly
mRNA splicing, via spliceosome
termination of RNA polymerase II transcription
histone mRNA metabolic process

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
U5 snRNP
U7 snRNP

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000414487
Coding exons: 5
Length: 8948
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	25	51.6	0.484	0.00000275	603
Missense (PolyPhen)		1	4.0504	0.24689		71
Synonymous	0.385	15	17.0	0.881	8.28e-7	155
Loss of Function	2.56	0	7.63	0.00	3.32e-7	89

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	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3'-end processing. May indirectly play a role in hair development. {ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:23246290, ECO:0000269|PubMed:23333303}.;

Recessive Scores

pRec: 0.466

Intolerance Scores

RVIS EVS: 0.12
RVIS percentile EVS: 62.38

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.999