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.

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.

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				3	6	9
missense			39		1	40
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	40	3	7

Variants in CRMP1

This is a list of pathogenic ClinVar variants found in the CRMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-5748087-C-T			Benign (Jun 25, 2018)
4-5748087-C-CCTTTG			Likely benign (Jan 20, 2019)
4-5748087-C-CGTTTG			Benign (Jun 17, 2020)
4-5748133-G-A		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Jun 02, 2023)
4-5748133-G-T		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Nov 09, 2023)
4-5748134-T-C		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Dec 02, 2023)
4-5748136-C-G		Ellis-van Creveld syndrome;Curry-Hall syndrome	Benign (Feb 01, 2024)
4-5748139-A-C		Ellis-van Creveld syndrome;Curry-Hall syndrome	Likely benign (Nov 24, 2023)
4-5748139-A-G		Ellis-van Creveld syndrome;Curry-Hall syndrome	Likely benign (Dec 30, 2023)
4-5748142-T-C		Ellis-van Creveld syndrome;Curry-Hall syndrome	Likely benign (Jul 02, 2021)
4-5748148-A-G		Ellis-van Creveld syndrome;Curry-Hall syndrome	Uncertain significance (Nov 08, 2021)
4-5748153-A-G		not specified • Ellis-van Creveld syndrome;Curry-Hall syndrome	Likely benign (Apr 07, 2023)
4-5748165-A-G		Ellis-van Creveld syndrome;Curry-Hall syndrome	Likely benign (Jul 06, 2021)
4-5748166-C-T		Curry-Hall syndrome;Ellis-van Creveld syndrome	Pathogenic (Jan 30, 2024)
4-5748177-T-C		not specified • Ellis-van Creveld syndrome • Ellis-van Creveld syndrome;Curry-Hall syndrome • Curry-Hall syndrome	Benign (Feb 01, 2024)
4-5748181-C-T		Ellis-van Creveld syndrome;Curry-Hall syndrome	Pathogenic (Nov 04, 2019)
4-5748190-C-T		Ellis-van Creveld syndrome • Curry-Hall syndrome;Ellis-van Creveld syndrome	Conflicting classifications of pathogenicity (Jan 31, 2024)
4-5748191-TTG-T		Curry-Hall syndrome;Ellis-van Creveld syndrome	Pathogenic (Jan 16, 2024)
4-5748193-G-GATCTT		Ellis-van Creveld syndrome	Likely pathogenic (Jan 25, 2022)
4-5748195-G-A		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Sep 19, 2022)
4-5748198-C-T		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Jun 09, 2023)
4-5748207-G-A		Ellis-van Creveld syndrome;Curry-Hall syndrome	Likely benign (Nov 24, 2023)
4-5748207-G-GAACATTC		Ellis-van Creveld syndrome	Likely pathogenic (Feb 25, 2022)
4-5748213-C-T		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Aug 29, 2023)
4-5748216-C-T		Curry-Hall syndrome;Ellis-van Creveld syndrome	Likely benign (Apr 22, 2023)

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