NGRN

neugrin, neurite outgrowth associated

Basic information

Region (hg38): 15:90265659-90275778

Links

ENSG00000182768 ∙ NCBI:51335 ∙ OMIM:616718 ∙ HGNC:18077 ∙ Uniprot:Q9NPE2 ∙ 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 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	2	2	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: gnomAD

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: 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

	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