NGRN
Basic information
Region (hg38): 15:90265659-90275778
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 NGRN 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 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 18 | 2 | 2 |
Variants in NGRN
This is a list of pathogenic ClinVar variants found in the NGRN region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-90265720-T-G | not specified | Uncertain significance (Jan 22, 2024) | ||
15-90265774-G-C | not specified | Uncertain significance (May 04, 2022) | ||
15-90265791-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
15-90265795-C-G | not specified | Uncertain significance (Jun 11, 2021) | ||
15-90265846-C-A | not specified | Uncertain significance (Feb 28, 2024) | ||
15-90266302-A-G | not specified | Uncertain significance (Dec 04, 2024) | ||
15-90266349-C-A | not specified | Uncertain significance (Jun 09, 2022) | ||
15-90266368-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
15-90266396-A-C | Benign (Jan 19, 2018) | |||
15-90271207-C-G | not specified | Likely benign (Mar 20, 2024) | ||
15-90271259-A-T | not specified | Uncertain significance (Jan 07, 2022) | ||
15-90271261-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
15-90271286-A-C | not specified | Uncertain significance (Nov 03, 2023) | ||
15-90271327-A-G | Benign (Nov 09, 2017) | |||
15-90271372-C-T | Likely benign (Sep 01, 2023) | |||
15-90271378-T-C | not specified | Uncertain significance (Dec 19, 2023) | ||
15-90271438-C-T | not specified | Uncertain significance (Oct 08, 2024) | ||
15-90271451-C-G | not specified | Uncertain significance (Sep 01, 2021) | ||
15-90271526-G-A | not specified | Uncertain significance (Mar 22, 2023) | ||
15-90271664-C-T | not specified | Uncertain significance (May 16, 2024) | ||
15-90271676-G-C | not specified | Uncertain significance (Jul 28, 2021) | ||
15-90271712-A-G | Benign (Jan 19, 2018) | |||
15-90271733-T-C | not specified | Uncertain significance (Dec 21, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NGRN | protein_coding | protein_coding | ENST00000379095 | 3 | 7573 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000779 | 0.787 | 125724 | 0 | 23 | 125747 | 0.0000915 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.451 | 169 | 153 | 1.10 | 0.00000732 | 1869 |
Missense in Polyphen | 37 | 37.4 | 0.98931 | 550 | ||
Synonymous | 0.174 | 63 | 64.8 | 0.972 | 0.00000317 | 598 |
Loss of Function | 1.05 | 6 | 9.51 | 0.631 | 5.03e-7 | 114 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000243 | 0.000242 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000133 | 0.000132 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000992 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays an essential role in mitochondrial ribosome biogenesis. As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mitochondrial ribosomal RNA (16S mt-rRNA), controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation of core subunits of the oxidative phosphorylation system. {ECO:0000269|PubMed:27667664}.;
Intolerance Scores
- loftool
- 0.739
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.22
Haploinsufficiency Scores
- pHI
- 0.0395
- hipred
- N
- hipred_score
- 0.145
- ghis
- 0.406
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.599
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ngrn
- 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
- neuron differentiation;positive regulation of mitochondrial translation
- Cellular component
- extracellular region;nucleus;mitochondrial membrane
- Molecular function
- RNA binding;rRNA binding