CHADL

chondroadherin like

Basic information

Region (hg38): 22:41229510-41240931

Links

ENSG00000100399 ∙ NCBI:150356 ∙ OMIM:616236 ∙ HGNC:25165 ∙ Uniprot:Q6NUI6 ∙ 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 CHADL gene.

• not_specified (140 variants)
• not_provided (5 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHADL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138481.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	4		5
missense			129	6		135
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	130	10	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHADL	protein_coding	protein_coding	ENST00000216241	6	11422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.89e-8	0.514	123358	0	2	123360	0.00000811

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	277	385	0.719	0.0000246	4654
Missense in Polyphen		89	130.49	0.68205		1755
Synonymous	3.41	132	192	0.687	0.0000122	1844
Loss of Function	0.997	14	18.6	0.751	9.60e-7	216

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential negative modulator of chondrocyte differentiation. Inhibits collagen fibrillogenesis in vitro. May influence chondrocyte's differentiation by acting on its cellular collagenous microenvironment. {ECO:0000269|PubMed:25451920}.

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0817

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chadl

Gene ontology

• Biological process: negative regulation of chondrocyte differentiation;negative regulation of collagen fibril organization
• Cellular component: extracellular space;extracellular matrix;collagen-containing extracellular matrix
• Molecular function: collagen binding;extracellular matrix structural constituent conferring compression resistance;collagen fibril binding