NEGR1

protein-coding

neuronal growth regulator 1, the group of I-set domain containing|IgLON cell adhesion molecules

Gene summary

Enables transmembrane transporter binding activity. Acts upstream of or within several processes, including cholesterol homeostasis; protein localization to plasma membrane raft; and regulation of protein stability. Located in late endosome and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173808.3

Inheritance

—

ClinVar variants

U:35B:7

Top phenotype

NEGR1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr1:71,395,943-72,282,539

External References & Databases

Ensembl (ENSG00000172260)

Transcript & Mutation Effects

hg38 • Region Span ~886.6 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 NEGR1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 6

NEGR1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173808.3. 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			2 clinvar	2 clinvar	2 clinvar	6
missense			32 clinvar	2 clinvar	1 clinvar	35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	4	3	42

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173808.3	RefSeq	NP_776169.2	7	MANE Select
ENST00000357731.10	Ensembl	ENSP00000350364.4	7	MANE Select
ENST00000306821.3	Ensembl	ENSP00000305938.3	6	Standard
ENST00000306821.4	Ensembl	ENSP00000305938.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell adhesion molecules (CAMs) - Homo sapiens (human)
Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

locomotory behavior
feeding behavior
positive regulation of neuron projection development
cell-cell adhesion

Molecular Function

protein binding

Cellular Component

extracellular region
plasma membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357731
Coding exons: 7
Length: 886795
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125747
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.64	135	200	0.674	0.0000103	2299
Missense (PolyPhen)		30	69.375	0.43243		762
Synonymous	-0.344	82	78.1	1.05	0.00000435	705
Loss of Function	3.80	1	18.8	0.0533	0.00000104	202

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in cell-adhesion. May function as a trans-neural growth-promoting factor in regenerative axon sprouting in the mammalian brain (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.316
RVIS EVS: -0.27
RVIS percentile EVS: 34.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.462

Gene Damage Prediction

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