NIPSNAP1

nipsnap homolog 1

Basic information

Region (hg38): 22:29554808-29581327

Links

ENSG00000184117 ∙ NCBI:8508 ∙ OMIM:603249 ∙ HGNC:7827 ∙ Uniprot:Q9BPW8 ∙ 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 NIPSNAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPSNAP1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in NIPSNAP1

This is a list of pathogenic ClinVar variants found in the NIPSNAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29555988-G-C		not specified	Uncertain significance (Nov 10, 2024)
22-29558920-C-G		not specified	Uncertain significance (Jan 29, 2025)
22-29558951-A-G		not specified	Uncertain significance (Jan 24, 2024)
22-29560814-T-C		not specified	Uncertain significance (Feb 10, 2022)
22-29560818-T-C		not specified	Uncertain significance (Mar 17, 2023)
22-29561531-T-C		not specified	Uncertain significance (Nov 08, 2022)
22-29561600-C-T		not specified	Uncertain significance (Aug 20, 2024)
22-29569249-T-C		not specified	Uncertain significance (May 29, 2024)
22-29570471-G-T		not specified	Uncertain significance (Jan 07, 2025)
22-29570474-C-T		not specified	Uncertain significance (Jan 21, 2025)
22-29570497-C-T		not specified	Uncertain significance (Oct 03, 2024)
22-29570529-G-T		not specified	Uncertain significance (Jun 17, 2024)
22-29581036-A-C		not specified	Uncertain significance (May 05, 2023)
22-29581061-T-C		not specified	Uncertain significance (Jan 18, 2023)
22-29581064-T-C		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPSNAP1	protein_coding	protein_coding	ENST00000216121	10	26530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.100	0.900	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	92	157	0.587	0.00000907	1845
Missense in Polyphen		11	31.82	0.34569		362
Synonymous	0.540	55	60.3	0.912	0.00000325	520
Loss of Function	3.18	6	22.1	0.271	0.00000131	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.548
• hipred: Y
• hipred_score: 0.662
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nipsnap1
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: sensory perception of pain
• Cellular component: mitochondrion;synaptic membrane
• Molecular function: protein binding;neurotransmitter binding