NSRP1

nuclear speckle splicing regulatory protein 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 17:30115520-30186475

Previous symbols: [ "CCDC55" ]

Links

ENSG00000126653 ∙ NCBI:84081 ∙ OMIM:616173 ∙ HGNC:25305 ∙ Uniprot:Q9H0G5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with spasticity, seizures, and brain abnormalities (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with spasticity, seizures, and brain abnormalities	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; Neurologic	34385670

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NSRP1 gene.

• Inborn genetic diseases (18 variants)
• not provided (4 variants)
• Neurodevelopmental disorder with spasticity, seizures, and brain abnormalities (2 variants)
• not specified (1 variants)
• Microcephaly;Seizure;Spasticity;Severe global developmental delay (1 variants)
• NSRP1-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSRP1 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			21			21
nonsense		1	1			2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	2	22	0	1

Highest pathogenic variant AF is 0.00000657

Variants in NSRP1

This is a list of pathogenic ClinVar variants found in the NSRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-30116845-T-C		not specified	Uncertain significance (Mar 28, 2024)
17-30116853-C-T		not specified	Uncertain significance (Nov 30, 2021)
17-30116854-C-G		not specified	Uncertain significance (Dec 21, 2023)
17-30117165-A-C			Benign (Jan 10, 2019)
17-30118083-T-G		not specified	Likely pathogenic (Sep 16, 2022)
17-30118090-A-G		not specified	Uncertain significance (Jan 26, 2023)
17-30118111-C-T		Microcephaly;Seizure;Spasticity;Severe global developmental delay • Neurodevelopmental disorder with spasticity, seizures, and brain abnormalities	Uncertain significance (Jul 21, 2019)
17-30172569-G-A		not specified	Uncertain significance (Apr 26, 2023)
17-30178091-G-C		not specified	Uncertain significance (May 05, 2023)
17-30178149-A-G		NSRP1-related disorder	Likely benign (Mar 18, 2022)
17-30179116-A-C		not specified	Uncertain significance (Jan 02, 2024)
17-30179153-A-G		not specified	Uncertain significance (Sep 17, 2021)
17-30179184-T-A			Uncertain significance (Apr 18, 2023)
17-30179202-A-C		not specified	Uncertain significance (Mar 16, 2022)
17-30179235-A-C			Uncertain significance (Apr 18, 2023)
17-30180953-G-A		not specified	Uncertain significance (May 05, 2023)
17-30181007-G-A		not specified	Uncertain significance (Oct 22, 2021)
17-30184686-A-G		not specified	Uncertain significance (Dec 26, 2023)
17-30184748-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-30184764-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-30184776-T-C		not specified	Uncertain significance (Jan 17, 2024)
17-30184904-C-T		not specified	Uncertain significance (Jun 01, 2023)
17-30184978-C-G		Neurodevelopmental disorder with spasticity, seizures, and brain abnormalities	Uncertain significance (Mar 13, 2023)
17-30184995-C-T		not specified	Uncertain significance (Nov 21, 2023)
17-30185001-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSRP1	protein_coding	protein_coding	ENST00000247026	7	70955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0121	0.988	125701	0	44	125745	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.147	273	280	0.975	0.0000137	3751
Missense in Polyphen		43	64.558	0.66607		905
Synonymous	-0.475	102	96.1	1.06	0.00000463	909
Loss of Function	3.16	8	25.1	0.319	0.00000125	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000518	0.000514
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000115	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000188	0.000185
Middle Eastern	0.000115	0.000109
South Asian	0.000296	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that mediates pre-mRNA alternative splicing regulation. {ECO:0000269|PubMed:21296756}.

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.493
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsrp1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;RNA splicing;developmental process
• Cellular component: nucleus;nucleoplasm;nuclear speck;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding