NRN1L

neuritin 1 like

Basic information

Region (hg38): 16:67884885-67888855

Links

ENSG00000188038 ∙ NCBI:123904 ∙ ∙ HGNC:29811 ∙ Uniprot:Q496H8 ∙ 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 NRN1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRN1L 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			9	2	2	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	2

Variants in NRN1L

This is a list of pathogenic ClinVar variants found in the NRN1L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-67884946-C-T		not specified	Uncertain significance (May 31, 2023)
16-67885752-C-T		not specified	Likely benign (Jul 12, 2023)
16-67885776-T-C		not specified	Uncertain significance (Jul 05, 2023)
16-67885805-C-T		not specified	Uncertain significance (Apr 05, 2023)
16-67885826-C-T		not specified	Uncertain significance (Apr 29, 2024)
16-67885827-G-A		not specified	Likely benign (Jan 20, 2025)
16-67885835-G-A		not specified	Uncertain significance (Dec 15, 2023)
16-67886084-C-G			Benign (Dec 31, 2019)
16-67886084-C-T		not specified	Uncertain significance (Nov 10, 2022)
16-67886106-C-A			not provided (-)
16-67886126-G-A		not specified	Likely benign (Dec 16, 2022)
16-67886131-C-T		not specified	Uncertain significance (Dec 17, 2021)
16-67886206-C-T			Benign (Apr 19, 2018)
16-67886227-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-67886246-G-A		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRN1L	protein_coding	protein_coding	ENST00000339176	3	4051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000952	0.359	125710	0	16	125726	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.315	121	112	1.08	0.00000744	1010
Missense in Polyphen		31	31.963	0.96987		317
Synonymous	-1.92	65	48.1	1.35	0.00000331	371
Loss of Function	-0.00384	6	5.99	1.00	3.35e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000339	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000557	0.0000528
Middle Eastern	0.000339	0.000326
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Intolerance Scores

• loftool: 0.258
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.44

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.123
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0932

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nrn1l
• Phenotype: normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: neuron projection extension
• Cellular component: extracellular region;extracellular space;plasma membrane;axon;anchored component of plasma membrane
• Molecular function: protein homodimerization activity;protein heterodimerization activity