CHAD

chondroadherin, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 17:50464496-50468906

Links

ENSG00000136457 ∙ NCBI:1101 ∙ OMIM:602178 ∙ HGNC:1909 ∙ Uniprot:O15335 ∙ 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 CHAD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHAD 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					2	2
missense			20		3	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	5

Variants in CHAD

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

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

Position	Type	Phenotype	Significance	ClinVar
17-50465305-C-A		not specified	Uncertain significance (Nov 10, 2024)
17-50465329-G-A			Benign (Jul 15, 2018)
17-50465331-G-A			Benign (Jul 15, 2018)
17-50465347-C-T		not specified	Uncertain significance (Oct 14, 2023)
17-50465348-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-50465353-G-T			Likely benign (Dec 01, 2024)
17-50465354-C-T		not specified	Uncertain significance (Aug 27, 2024)
17-50465366-G-A		not specified	Uncertain significance (Feb 07, 2025)
17-50465708-G-A		not specified	Uncertain significance (May 22, 2023)
17-50465812-T-A		not specified	Uncertain significance (Mar 10, 2025)
17-50465849-C-T		not specified	Uncertain significance (Jul 14, 2024)
17-50465857-G-C		not specified	Uncertain significance (Sep 02, 2024)
17-50468138-G-A			Benign (Jun 27, 2018)
17-50468149-T-C		not specified	Uncertain significance (Feb 04, 2025)
17-50468191-G-A		not specified	Uncertain significance (May 04, 2023)
17-50468222-C-T		not specified	Uncertain significance (Jan 24, 2023)
17-50468243-G-C			Benign (Jul 15, 2018)
17-50468251-G-A		not specified	Uncertain significance (Sep 24, 2024)
17-50468326-C-T		not specified	Uncertain significance (Mar 21, 2023)
17-50468342-T-C		not specified	Uncertain significance (Mar 20, 2023)
17-50468365-A-G		not specified	Uncertain significance (Jan 08, 2025)
17-50468380-G-A		not specified	Uncertain significance (Jun 22, 2024)
17-50468454-G-T		not specified	Uncertain significance (Mar 21, 2023)
17-50468506-T-C		not specified	Uncertain significance (Jun 28, 2024)
17-50468595-G-A		not specified	Likely benign (Jan 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHAD	protein_coding	protein_coding	ENST00000508540	3	4471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00698	0.926	125726	0	20	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.675	206	235	0.876	0.0000158	2313
Missense in Polyphen		94	101.67	0.92454		977
Synonymous	2.14	83	112	0.743	0.00000752	764
Loss of Function	1.58	5	10.5	0.475	4.47e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes attachment of chondrocytes, fibroblasts, and osteoblasts. This binding is mediated (at least for chondrocytes and fibroblasts) by the integrin alpha(2)beta(1). May play an important role in the regulation of chondrocyte growth and proliferation (By similarity). {ECO:0000250}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.224

Intolerance Scores

• loftool: 0.201
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.303
• hipred: Y
• hipred_score: 0.507
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chad
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; skeleton phenotype

Gene ontology

• Biological process: bone development;negative regulation of bone trabecula formation
• Cellular component: extracellular space;extracellular matrix