NGRN

neugrin, neurite outgrowth associated

Basic information

Region (hg38): 15:90265659-90275778

Links

ENSG00000182768NCBI:51335OMIM:616718HGNC:18077Uniprot:Q9NPE2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NGRN gene.

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
clinvar
2
clinvar
2
clinvar
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)3199366
15-90265774-G-C not specified Uncertain significance (May 04, 2022)2287395
15-90265791-G-A not specified Uncertain significance (Mar 01, 2023)2492754
15-90265795-C-G not specified Uncertain significance (Jun 11, 2021)2229867
15-90265846-C-A not specified Uncertain significance (Feb 28, 2024)3199322
15-90266302-A-G not specified Uncertain significance (Dec 04, 2024)3405355
15-90266349-C-A not specified Uncertain significance (Jun 09, 2022)2386621
15-90266368-C-T not specified Uncertain significance (Mar 06, 2023)2455170
15-90266396-A-C Benign (Jan 19, 2018)776942
15-90271207-C-G not specified Likely benign (Mar 20, 2024)3299614
15-90271259-A-T not specified Uncertain significance (Jan 07, 2022)2271063
15-90271261-G-A not specified Uncertain significance (Dec 01, 2022)2331467
15-90271286-A-C not specified Uncertain significance (Nov 03, 2023)3199338
15-90271327-A-G Benign (Nov 09, 2017)784619
15-90271372-C-T Likely benign (Sep 01, 2023)2645705
15-90271378-T-C not specified Uncertain significance (Dec 19, 2023)3199343
15-90271438-C-T not specified Uncertain significance (Oct 08, 2024)3405354
15-90271451-C-G not specified Uncertain significance (Sep 01, 2021)2248369
15-90271526-G-A not specified Uncertain significance (Mar 22, 2023)2528335
15-90271664-C-T not specified Uncertain significance (May 16, 2024)3299613
15-90271676-G-C not specified Uncertain significance (Jul 28, 2021)2239845
15-90271712-A-G Benign (Jan 19, 2018)776943
15-90271733-T-C not specified Uncertain significance (Dec 21, 2023)3199359

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NGRNprotein_codingprotein_codingENST00000379095 37573
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0007790.7871257240231257470.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4511691531.100.000007321869
Missense in Polyphen3737.40.98931550
Synonymous0.1746364.80.9720.00000317598
Loss of Function1.0569.510.6315.03e-7114

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002430.000242
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001330.000132
Middle Eastern0.000.00
South Asian0.00009920.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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