NIPSNAP2

nipsnap homolog 2

Basic information

Region (hg38): 7:55951793-56000181

Previous symbols: [ "GBAS" ]

Links

ENSG00000146729NCBI:2631OMIM:603004HGNC:4179Uniprot:O75323AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)3398301
7-55953250-G-A not specified Uncertain significance (May 03, 2023)2542530
7-55953254-C-G not specified Uncertain significance (Aug 22, 2023)2588834
7-55953299-T-G not specified Uncertain significance (Oct 18, 2021)2330886
7-55953308-A-G not specified Uncertain significance (Jul 12, 2023)2596483
7-55954903-C-G Likely benign (Jun 01, 2023)2657514
7-55954931-A-G not specified Uncertain significance (Jul 14, 2024)3398300
7-55954964-T-C not specified Uncertain significance (Dec 07, 2024)3398302
7-55955038-G-A not specified Likely benign (Oct 05, 2021)2205768
7-55955075-G-A not specified Uncertain significance (Feb 22, 2023)2487542
7-55955141-A-G not specified Uncertain significance (May 03, 2023)2537924
7-55964620-G-C not specified Uncertain significance (May 31, 2023)2553678
7-55964653-G-C not specified Uncertain significance (Jun 17, 2022)3200188
7-55964655-G-T not specified Uncertain significance (Dec 07, 2021)3200190
7-55964668-G-A not specified Uncertain significance (Feb 02, 2022)3200191
7-55964670-G-C not specified Uncertain significance (Jun 18, 2024)3299818
7-55964688-C-A not specified Uncertain significance (Dec 27, 2023)3200194
7-55978169-C-G not specified Uncertain significance (Apr 16, 2024)3299814
7-55978221-A-G not specified Uncertain significance (May 26, 2024)3200184
7-55978223-C-G not specified Uncertain significance (Jun 21, 2022)3200185
7-55978356-A-G not specified Uncertain significance (May 08, 2024)3299813
7-55978377-A-G not specified Uncertain significance (May 07, 2024)3299815
7-55982225-A-G not specified Uncertain significance (Sep 24, 2024)3200186
7-55982237-A-C not specified Uncertain significance (Jul 22, 2022)3200187
7-55983743-C-T not specified Uncertain significance (May 15, 2024)3299817

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NIPSNAP2protein_codingprotein_codingENST00000322090 1048389
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.34e-80.5881257010461257470.000183
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.34991440.6870.000007841866
Missense in Polyphen2439.0510.61458421
Synonymous-0.8546052.21.150.00000296519
Loss of Function1.151520.60.7270.00000103234

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002390.000239
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.00004630.0000462
European (Non-Finnish)0.0002910.000281
Middle Eastern0.0002720.000272
South Asian0.00006530.0000653
Other0.000.00

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

loftool
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_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Nipsnap2
Phenotype

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