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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 7.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001033088.3	NP_001028260.2	3	yes	-
ENST00000379095.5	ENSP00000368389.4	3	yes	-
ENST00000411845.3	ENSP00000480153.1	2	-	-
ENST00000885215.1	ENSP00000555274.1	2	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (49 variants)
• not_provided (4 variants)

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. These statistics are base on transcript: NM_001033088.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			45	4	2	51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	4	3

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
		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

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

Gene ontology

• Biological process: neuron differentiation;positive regulation of mitochondrial translation
• Cellular component: extracellular region;nucleus;mitochondrial membrane
• Molecular function: RNA binding;rRNA binding