SNIP1

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

Basic information

Region (hg38): 1:37534448-37554293

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.

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.

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			2	46	4	52
missense			117	6	1	124
nonsense			5			5
start loss						0
frameshift			3			3
inframe indel			7			7
splice donor/acceptor (+/-2bp)						0
splice region			3	8	2	13
non coding				5		5
Total	0	0	134	57	5

Variants in SNIP1

This is a list of pathogenic ClinVar variants found in the SNIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37537761-A-G			Uncertain significance (Mar 17, 2023)
1-37537761-ACTT-A			Uncertain significance (Jan 08, 2021)
1-37537766-TTCC-T			Uncertain significance (Jan 25, 2024)
1-37537769-C-T			Likely benign (Jan 19, 2024)
1-37537775-CTCCTCA-C			Uncertain significance (Jun 13, 2022)
1-37537778-C-G			Uncertain significance (Oct 03, 2023)
1-37537778-CTCA-C			Uncertain significance (Oct 13, 2023)
1-37537781-A-C		not specified	Uncertain significance (May 06, 2024)
1-37537783-C-T		Psychomotor retardation, epilepsy, and craniofacial dysmorphism	Uncertain significance (Dec 01, 2023)
1-37537786-C-T		not specified	Uncertain significance (Mar 30, 2024)
1-37537787-G-A			Likely benign (Jun 05, 2023)
1-37537791-T-C		not specified	Uncertain significance (May 26, 2024)
1-37537793-T-C			Likely benign (Feb 08, 2022)
1-37537794-T-C			Uncertain significance (Jan 04, 2024)
1-37537796-CCTGT-C		Psychomotor retardation, epilepsy, and craniofacial dysmorphism	Uncertain significance (Jun 28, 2021)
1-37537804-T-C			Uncertain significance (Jul 12, 2022)
1-37537815-T-C			Uncertain significance (Jan 02, 2022)
1-37537817-C-T			Likely benign (Nov 28, 2023)
1-37537818-G-A		not specified	Uncertain significance (Jun 18, 2024)
1-37537820-C-A			Likely benign (Oct 04, 2022)
1-37537820-C-T			Likely benign (Aug 15, 2022)
1-37537821-G-A		not specified	Uncertain significance (Oct 13, 2023)
1-37537826-A-G			Likely benign (Jun 01, 2022)
1-37537831-G-A			Uncertain significance (Sep 30, 2023)
1-37537833-A-G			Uncertain significance (Nov 18, 2022)

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