CRMP1

protein-coding

collapsin response mediator protein 1, the group of M38 metallopeptidases

Gene summary

This gene encodes a member of a family of cytosolic phosphoproteins expressed exclusively in the nervous system. The encoded protein is thought to be a part of the semaphorin signal transduction pathway implicated in semaphorin-induced growth cone collapse during neural development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001014809.3

Inheritance

—

ClinVar variants

P:1U:110B:13

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr4:5,748,084-5,893,086

External References & Databases

Ensembl (ENSG00000072832)

Transcript & Mutation Effects

hg38 • Region Span ~145.0 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 CRMP1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 16

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Neurodevelopmental disorderTotal: 1

CRMP1-related neurodevelopmental disorderTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001014809.3. 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			1 clinvar	6 clinvar	6 clinvar	13
missense			105 clinvar		1 clinvar	106
nonsense			1 clinvar			1
start loss						0
frameshift		1 clinvar	2 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	110	6	7	124

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001014809.3	RefSeq	NP_001014809.1	14	MANE Select
ENST00000324989.12	Ensembl	ENSP00000321606.7	14	MANE Select
NM_001288661.2	RefSeq	NP_001275590.1	14	Standard
NM_001288662.1	RefSeq	NP_001275591.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Developmental Biology
Semaphorin interactions
Axon guidance
CRMPs in Sema3A signaling

Biological Process

microtubule cytoskeleton organization
nucleobase-containing compound metabolic process
nervous system development
axon guidance
negative regulation of neuron projection development

Molecular Function

protein binding
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
filamin binding

Cellular Component

nucleus
centrosome
spindle
cytosol
midbody

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000324989
Coding exons: 14
Length: 144975
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125747
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.41	244	376	0.650	0.0000231	4430
Missense (PolyPhen)		81	165.07	0.49069		1676
Synonymous	-0.815	174	161	1.08	0.0000117	1388
Loss of Function	4.34	3	27.6	0.109	0.00000126	350

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. May participate in cytokinesis. {ECO:0000269|PubMed:11562390, ECO:0000269|PubMed:19799413}.;

Recessive Scores

pRec: 0.163

Intolerance Scores

LoFtool: 0.0145
RVIS EVS: -0.75
RVIS percentile EVS: 13.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.178

Gene Damage Prediction

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