CHODL

chondrolectin, the group of C-type lectin domain containing

Basic information

Region (hg38): 21:17901263-18267373

Previous symbols: [ "C21orf68" ]

Links

ENSG00000154645 ∙ NCBI:140578 ∙ OMIM:607247 ∙ HGNC:17807 ∙ Uniprot:Q9H9P2 ∙ 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 CHODL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHODL 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in CHODL

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

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

Position	Type	Phenotype	Significance	ClinVar
21-18245261-T-A		not specified	Uncertain significance (Sep 19, 2022)
21-18245270-G-T		not specified	Uncertain significance (Aug 13, 2021)
21-18256556-G-A		not specified	Uncertain significance (Mar 22, 2023)
21-18256734-G-A		not specified	Uncertain significance (Dec 19, 2022)
21-18256776-C-T		not specified	Uncertain significance (Feb 06, 2023)
21-18257038-C-T		not specified	Uncertain significance (Nov 13, 2023)
21-18257041-A-G		not specified	Uncertain significance (Dec 18, 2023)
21-18260215-C-T		not specified	Uncertain significance (Aug 04, 2022)
21-18262820-A-C		not specified	Uncertain significance (Dec 16, 2023)
21-18265956-A-T		not specified	Uncertain significance (Dec 12, 2023)
21-18266029-G-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHODL	protein_coding	protein_coding	ENST00000299295	6	366111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.15e-8	0.265	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0511	144	142	1.01	0.00000663	1788
Missense in Polyphen		46	56.595	0.81279		710
Synonymous	-0.220	51	49.0	1.04	0.00000225	513
Loss of Function	0.525	13	15.2	0.855	8.17e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000356	0.000356
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000110	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the development of the nervous system such as in neurite outgrowth and elongation. May be involved in motor axon growth and guidance. {ECO:0000250|UniProtKB:Q568T5, ECO:0000250|UniProtKB:Q9CXM0}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.713
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.238
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chodl

Zebrafish Information Network

• Gene name: chodl
• Affected structure: CaP motoneuron
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: muscle organ development;regulation of neuron projection development;positive regulation of axonogenesis
• Cellular component: cytoplasm;endoplasmic reticulum membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: hyaluronic acid binding;carbohydrate binding