SNIP1

Smad nuclear interacting protein 1, the group of Spliceosomal P complex

Basic information

Region (hg38): 1:37534449-37554293

Links

ENSG00000163877

∙ NCBI:79753 ∙ OMIM:608241 ∙ HGNC:30587 ∙ Uniprot:Q8TAD8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

psychomotor retardation, epilepsy, and craniofacial dysmorphism (Limited), mode of inheritance: AR
psychomotor retardation, epilepsy, and craniofacial dysmorphism (Limited), mode of inheritance: AR
psychomotor retardation, epilepsy, and craniofacial dysmorphism (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with hypotonia, craniofacial abnormalities, and seizures	AR	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	Craniofacial; Musculoskeletal; Neurologic	22279524

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNIP1 gene.

not_provided (233 variants)
not_specified (49 variants)
Psychomotor_retardation,_epilepsy,_and_craniofacial_dysmorphism (10 variants)
SNIP1-related_disorder (4 variants)
Predisposition_to_dissection (1 variants)
Self-limited_epilepsy_with_centrotemporal_spikes (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024700.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				56 clinvar	3 clinvar	59
missense		1 clinvar	145 clinvar	12 clinvar	1 clinvar	159
nonsense		1 clinvar	5 clinvar			6
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	0	2	154	68	4

Highest pathogenic variant AF is 0.000009293104

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNIP1	protein_coding	protein_coding	ENST00000296215	4	19854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.422	0.578	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	201	257	0.783	0.0000163	2559
Missense in Polyphen		33	61.892	0.53319		607
Synonymous	1.26	79	94.6	0.835	0.00000539	809
Loss of Function	3.10	4	18.3	0.218	0.00000124	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000589	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000631	0.0000615
Middle Eastern	0.0000589	0.0000544
South Asian	0.0000403	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Down-regulates NF-kappa-B signaling by competing with RELA for CREBBP/EP300 binding. Involved in the microRNA (miRNA) biogenesis. May be involved in cyclin-D1/CCND1 mRNA stability through the SNARP complex which associates with both the 3'end of the CCND1 gene and its mRNA. {ECO:0000269|PubMed:11567019, ECO:0000269|PubMed:15378006, ECO:0000269|PubMed:18632581, ECO:0000269|PubMed:18794151}.;
Disease: DISEASE: Psychomotor retardation, epilepsy, and craniofacial dysmorphism (PMRED) [MIM:614501]: A disease characterized by severe psychomotor retardation, intractable seizures, dysmorphic features, and a lumpy skull surface. Patients are hypotonic and have poor feeding in the neonatal period. {ECO:0000269|PubMed:22279524}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: TGF-Ncore;TGF-beta Signaling Pathway;TGF_beta_Receptor;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

pRec: 0.0973

Intolerance Scores

loftool: 0.251
rvis_EVS: 0.13
rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

pHI: 0.617
hipred: Y
hipred_score: 0.825
ghis: 0.560

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Snip1
Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype;

Gene ontology

Biological process: regulation of transcription, DNA-templated;I-kappaB kinase/NF-kappaB signaling;production of miRNAs involved in gene silencing by miRNA
Cellular component: nucleus;nucleoplasm;cytosol
Molecular function: RNA binding;mRNA binding;protein binding