SNRPE

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

Basic information

Region (hg38): 1:203861598-203871152

Links

ENSG00000182004 ∙ NCBI:6635 ∙ OMIM:128260 ∙ HGNC:11161 ∙ Uniprot:P62304 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypotrichosis 11 (Strong), mode of inheritance: AD
• hypotrichosis 11 (Limited), mode of inheritance: AD
• hypotrichosis simplex (Supportive), mode of inheritance: AD
• hypotrichosis 11 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotrichosis 11	AD	General	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	Dermatologic	23246290

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNRPE gene.

• not provided (3 variants)
• Inborn genetic diseases (2 variants)
• Hypotrichosis 11 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPE 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			2			2
nonsense						0
start loss		1	1			2
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	1	3	1	0

Variants in SNRPE

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

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

Position	Type	Phenotype	Significance	ClinVar
1-203861657-A-G		SNRPE-related disorder	Likely benign (Mar 21, 2019)
1-203861660-A-G		Hypotrichosis 11	Pathogenic/Likely pathogenic (Jun 28, 2022)
1-203861660-A-T			Uncertain significance (Dec 03, 2021)
1-203861673-G-C			Uncertain significance (May 29, 2023)
1-203861715-T-A		Hypotrichosis 11	Pathogenic (Apr 01, 2024)
1-203861723-G-A		SNRPE-related disorder	Likely benign (Jun 11, 2019)
1-203861932-C-T		SNRPE-related disorder	Likely benign (May 24, 2019)
1-203861936-A-G		SNRPE-related disorder	Benign (Jul 15, 2019)
1-203863700-A-C		not specified	Uncertain significance (Jun 29, 2022)
1-203863706-G-A		not specified	Uncertain significance (Aug 10, 2023)
1-203863714-G-A		Hypotrichosis 11	Pathogenic (Jan 10, 2013)
1-203863716-C-A			Likely benign (Jan 28, 2023)
1-203863736-A-G			Likely benign (Sep 10, 2022)
1-203865117-T-C		Hypotrichosis 11	Pathogenic (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPE	protein_coding	protein_coding	ENST00000414487	5	8948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.906	0.0932	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	25	51.6	0.484	0.00000275	603
Missense in 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

LoF frequencies by population

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

dbNSFP

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}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);snRNP Assembly;RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Metabolism of non-coding RNA;SLBP independent Processing of Histone Pre-mRNAs;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.466

Intolerance Scores

• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.739
• ghis: 0.729

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Mouse Genome Informatics

• Gene name: Snrpe
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: spliceosomal complex assembly;spliceosomal snRNP assembly;mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;histone mRNA metabolic process;hair cycle;import into nucleus
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U5 snRNP;U7 snRNP;U1 snRNP;U2 snRNP;U4 snRNP;U12-type spliceosomal complex;telomerase holoenzyme complex;cytosol;small nuclear ribonucleoprotein complex;methylosome;pICln-Sm protein complex;SMN-Sm protein complex;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding