SNRPF

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

Basic information

Region (hg38): 12:95858951-95903828

Links

ENSG00000139343 ∙ NCBI:6636 ∙ OMIM:603541 ∙ HGNC:11162 ∙ Uniprot:P62306 ∙ 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 SNRPF gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRPF 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			24	1		25
Total	0	0	24	1	0

Variants in SNRPF

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

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

Position	Type	Phenotype	Significance	ClinVar
12-95867122-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-95867189-A-G		not specified	Likely benign (Feb 27, 2024)
12-95869485-T-C		not specified	Uncertain significance (May 31, 2023)
12-95869499-A-G		not specified	Uncertain significance (May 24, 2024)
12-95869500-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-95869568-C-T		not specified	Uncertain significance (Apr 08, 2024)
12-95872262-G-A		not specified	Uncertain significance (Oct 05, 2022)
12-95872279-A-T		not specified	Uncertain significance (Jun 21, 2021)
12-95872312-A-G		not specified	Uncertain significance (May 09, 2022)
12-95872345-C-T		not specified	Uncertain significance (Oct 17, 2023)
12-95872346-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-95872385-C-T		not specified	Likely benign (Oct 05, 2021)
12-95872386-G-T		not specified	Uncertain significance (Jul 20, 2021)
12-95878236-A-G		not specified	Uncertain significance (Dec 14, 2022)
12-95878246-G-T		not specified	Uncertain significance (Sep 20, 2023)
12-95878248-T-C		not specified	Likely benign (Feb 17, 2024)
12-95878269-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-95878278-T-G		not specified	Uncertain significance (Apr 04, 2024)
12-95878285-C-T		not specified	Uncertain significance (Nov 07, 2023)
12-95878308-A-C		not specified	Uncertain significance (Mar 18, 2024)
12-95878309-T-C		not specified	Uncertain significance (Sep 16, 2021)
12-95878326-A-G		not specified	Uncertain significance (Apr 07, 2022)
12-95878335-A-G		not specified	Uncertain significance (Dec 19, 2022)
12-95878337-G-C		not specified	Uncertain significance (Mar 31, 2023)
12-95879653-T-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRPF	protein_coding	protein_coding	ENST00000266735	4	44901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.795	0.200	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	9	44.2	0.203	0.00000188	562
Missense in Polyphen		3	9.3968	0.31926		134
Synonymous	0.285	13	14.4	0.904	6.16e-7	151
Loss of Function	2.12	0	5.24	0.00	2.19e-7	70

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. {ECO:0000269|PubMed:18984161, 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)

Intolerance Scores

• rvis_EVS: 0.1
• rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

• pHI: 0.818
• hipred: Y
• hipred_score: 0.807
• ghis: 0.661

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Snrpf

Zebrafish Information Network

• Gene name: snrpf
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: spliceosomal snRNP assembly;mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;histone mRNA metabolic process;RNA splicing;import into nucleus
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;U7 snRNP;U1 snRNP;U4 snRNP;U12-type spliceosomal complex;small nucleolar ribonucleoprotein 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