NIPSNAP2
Basic information
Region (hg38): 7:55951793-56000181
Previous symbols: [ "GBAS" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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:
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:
- 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