CRMP1

collapsin response mediator protein 1, the group of M38 metallopeptidases

Basic information

Region (hg38): 4:5748084-5893086

Links

ENSG00000072832

∙ NCBI:1400 ∙ OMIM:602462 ∙ HGNC:2365 ∙ Uniprot:Q14194 ∙ 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 CRMP1 gene.

not_specified (87 variants)
not_provided (13 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
See_cases (1 variants)
CRMP1-related_neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRMP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001014809.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	6 clinvar	11
missense			87 clinvar		1 clinvar	88
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	1	88	5	7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRMP1	protein_coding	protein_coding	ENST00000324989	14	144975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00827	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.41	244	376	0.650	0.0000231	4430
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000615
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.;
Pathway: Developmental Biology;Semaphorin interactions;Axon guidance;CRMPs in Sema3A signaling (Consensus)

Recessive Scores

pRec: 0.163

Intolerance Scores

loftool: 0.0145
rvis_EVS: -0.75
rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

pHI: 0.533
hipred: Y
hipred_score: 0.851
ghis: 0.596

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.178

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Crmp1
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype;

Gene ontology

Biological process: microtubule cytoskeleton organization;nucleobase-containing compound metabolic process;nervous system development;axon guidance;negative regulation of neuron projection development;negative regulation of actin filament binding
Cellular component: nucleus;centrosome;spindle;cytosol;midbody
Molecular function: protein binding;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;filamin binding