NRN1L

protein-coding

neuritin 1 like

Gene summary

The protein encoded by this gene is extracellular and enhances both neurite growth and neuronal survival. The encoded protein is found both as a GPI anchored membrane-bound form and as a secreted form. This activity-related ligand functions as a homodimer or heterodimer. [provided by RefSeq, Feb 2017]

MANE transcript

NM_198443.2

Inheritance

—

ClinVar variants

U:28B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr16:67,884,885-67,888,855

External References & Databases

Ensembl (ENSG00000188038)

Transcript & Mutation Effects

hg38 • Region Span ~4.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NRN1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198443.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			27 clinvar	3 clinvar	2 clinvar	32
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	28	3	2	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198443.2	RefSeq	NP_940845.1	3	MANE Select
ENST00000339176.8	Ensembl	ENSP00000342411.3	3	MANE Select
NM_001348682.2	RefSeq	NP_001335611.1	3	Standard
ENST00000576147.1	Ensembl	ENSP00000464568.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

neuron projection extension

Molecular Function

protein homodimerization activity
protein heterodimerization activity

Cellular Component

extracellular region
extracellular space
plasma membrane
axon
anchored component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339176
Coding exons: 3
Length: 4051
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125726
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.315	121	112	1.08	0.00000744	1010
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.258
RVIS EVS: 0.91
RVIS percentile EVS: 89.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0932

Gene Damage Prediction

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