NIPSNAP2

nipsnap homolog 2

Basic information

Region (hg38): 7:55951793-56000181

Previous symbols: [ "GBAS" ]

Links

ENSG00000146729 ∙ NCBI:2631 ∙ OMIM:603004 ∙ HGNC:4179 ∙ Uniprot:O75323 ∙ 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 NIPSNAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIPSNAP2 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in NIPSNAP2

This is a list of pathogenic ClinVar variants found in the NIPSNAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-55953248-T-C		not specified	Uncertain significance (Sep 09, 2024)
7-55953250-G-A		not specified	Uncertain significance (May 03, 2023)
7-55953254-C-G		not specified	Uncertain significance (Aug 22, 2023)
7-55953299-T-G		not specified	Uncertain significance (Oct 18, 2021)
7-55953308-A-G		not specified	Uncertain significance (Jul 12, 2023)
7-55954903-C-G			Likely benign (Jun 01, 2023)
7-55954931-A-G		not specified	Uncertain significance (Jul 14, 2024)
7-55954964-T-C		not specified	Uncertain significance (Dec 07, 2024)
7-55955038-G-A		not specified	Likely benign (Oct 05, 2021)
7-55955075-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-55955141-A-G		not specified	Uncertain significance (May 03, 2023)
7-55964620-G-C		not specified	Uncertain significance (May 31, 2023)
7-55964653-G-C		not specified	Uncertain significance (Jun 17, 2022)
7-55964655-G-T		not specified	Uncertain significance (Dec 07, 2021)
7-55964668-G-A		not specified	Uncertain significance (Feb 02, 2022)
7-55964670-G-C		not specified	Uncertain significance (Jun 18, 2024)
7-55964688-C-A		not specified	Uncertain significance (Dec 27, 2023)
7-55978169-C-G		not specified	Uncertain significance (Apr 16, 2024)
7-55978221-A-G		not specified	Uncertain significance (May 26, 2024)
7-55978223-C-G		not specified	Uncertain significance (Jun 21, 2022)
7-55978356-A-G		not specified	Uncertain significance (May 08, 2024)
7-55978377-A-G		not specified	Uncertain significance (May 07, 2024)
7-55982225-A-G		not specified	Uncertain significance (Sep 24, 2024)
7-55982237-A-C		not specified	Uncertain significance (Jul 22, 2022)
7-55983743-C-T		not specified	Uncertain significance (May 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIPSNAP2	protein_coding	protein_coding	ENST00000322090	10	48389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-8	0.588	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	99	144	0.687	0.00000784	1866
Missense in Polyphen		24	39.051	0.61458		421
Synonymous	-0.854	60	52.2	1.15	0.00000296	519
Loss of Function	1.15	15	20.6	0.727	0.00000103	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000291	0.000281
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a positive regulator of L-type calcium channels. {ECO:0000250|UniProtKB:O55126}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.617
• ghis: 0.629

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Nipsnap2

Gene ontology

• Biological process: oxidative phosphorylation;mitochondrion organization;positive regulation of high voltage-gated calcium channel activity
• Cellular component: mitochondrion;mitochondrial outer membrane
• Molecular function: protein binding