CHL1

cell adhesion molecule L1 like, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 3:196762-409417

Links

ENSG00000134121 ∙ NCBI:10752 ∙ OMIM:607416 ∙ HGNC:1939 ∙ Uniprot:O00533 ∙ 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 CHL1 gene.

• Inborn genetic diseases (67 variants)
• not provided (54 variants)
• not specified (1 variants)
• CHL1-related condition (1 variants)
• Seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHL1 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				16	8	24
missense			64	14	4	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2	2	5
non coding				2	4	6
Total	0	0	64	32	16

Variants in CHL1

This is a list of pathogenic ClinVar variants found in the CHL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-319781-A-G		Seizure	Uncertain significance (Jan 01, 2019)
3-319783-C-A		not specified	Uncertain significance (Jul 05, 2023)
3-319804-C-G		CHL1-related disorder	Likely benign (Dec 31, 2019)
3-319812-A-G			Likely benign (Jul 10, 2018)
3-319825-C-T		CHL1-related disorder	Benign (Sep 24, 2019)
3-319864-T-G			Benign (Dec 31, 2019)
3-325956-T-A		CHL1-related disorder	Benign (Jul 10, 2019)
3-325962-A-G		not specified	Uncertain significance (Apr 12, 2023)
3-325995-T-C		not specified	Conflicting classifications of pathogenicity (Jun 22, 2021)
3-326022-A-G		CHL1-related disorder	Likely benign (Feb 21, 2023)
3-326061-C-T		not specified	Uncertain significance (Aug 16, 2022)
3-326074-G-C		CHL1-related disorder	Benign (Apr 12, 2022)
3-328173-G-A			Benign (Dec 31, 2019)
3-328209-C-T			Likely benign (Feb 09, 2018)
3-328247-G-A		not specified	Likely benign (Dec 21, 2023)
3-328248-G-A			Benign (Dec 31, 2019)
3-328267-A-G		not specified	Uncertain significance (May 05, 2023)
3-328292-G-A			Likely benign (Dec 07, 2019)
3-328292-G-T			Likely benign (Dec 07, 2019)
3-328363-T-G		CHL1-related disorder	Likely benign (Nov 30, 2020)
3-340832-G-A		not specified	Uncertain significance (May 17, 2023)
3-340846-A-C			Likely benign (Dec 31, 2019)
3-340848-A-G		not specified	Uncertain significance (Sep 22, 2023)
3-341925-C-T			Likely benign (Dec 24, 2018)
3-341973-C-T		CHL1-related disorder	Likely benign (May 08, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHL1	protein_coding	protein_coding	ENST00000256509	26	212812

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.89e-12	1.00	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	785	647	1.21	0.0000327	8005
Missense in Polyphen		243	247.66	0.98117		3137
Synonymous	-3.21	297	234	1.27	0.0000130	2288
Loss of Function	3.83	29	61.4	0.472	0.00000270	827

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000869	0.000866
Ashkenazi Jewish	0.000317	0.000298
East Asian	0.0000560	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000178	0.000176
Middle Eastern	0.0000560	0.0000544
South Asian	0.000166	0.000163
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Extracellular matrix and cell adhesion protein that plays a role in nervous system development and in synaptic plasticity. Both soluble and membranous forms promote neurite outgrowth of cerebellar and hippocampal neurons and suppress neuronal cell death. Plays a role in neuronal positioning of pyramidal neurons and in regulation of both the number of interneurons and the efficacy of GABAergic synapses. May play a role in regulating cell migration in nerve regeneration and cortical development. Potentiates integrin-dependent cell migration towards extracellular matrix proteins. Recruits ANK3 to the plasma membrane (By similarity). {ECO:0000250}.
• Pathway: Splicing factor NOVA regulated synaptic proteins;Developmental Biology;CHL1 interactions;L1CAM interactions;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.0966

Intolerance Scores

• loftool: 0.341
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.92

Haploinsufficiency Scores

• pHI: 0.392
• hipred: Y
• hipred_score: 0.604
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chl1
• Phenotype: 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); craniofacial phenotype; taste/olfaction phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: neuron migration;cell adhesion;signal transduction;axon guidance;adult locomotory behavior;exploration behavior;negative regulation of neuron apoptotic process;cognition
• Cellular component: plasma membrane;integral component of membrane;dendrite;apical part of cell;extracellular exosome
• Molecular function: protease binding