CHRD

chordin, the group of Chordin family

Basic information

Region (hg38): 3:184380054-184390736

Links

ENSG00000090539 ∙ NCBI:8646 ∙ OMIM:603475 ∙ HGNC:1949 ∙ Uniprot:Q9H2X0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital heart disease (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHRD gene.

• not_specified (158 variants)
• not_provided (9 variants)
• Anophthalmia-microphthalmia_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRD gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003741.4. 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			4	2	3	9
missense			155	8	1	164
nonsense			1			1
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)			5			5
Total	0	0	167	10	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRD	protein_coding	protein_coding	ENST00000204604	23	10664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	462	559	0.826	0.0000335	5937
Missense in Polyphen		206	258.78	0.79604		2724
Synonymous	-0.333	239	233	1.03	0.0000134	2088
Loss of Function	4.26	17	49.3	0.345	0.00000272	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000554	0.000478
Ashkenazi Jewish	0.000798	0.000794
East Asian	0.000163	0.000163
Finnish	0.000311	0.000277
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dorsalizing factor. Key developmental protein that dorsalizes early vertebrate embryonic tissues by binding to ventralizing TGF-beta family bone morphogenetic proteins (BMPs) and sequestering them in latent complexes (By similarity). {ECO:0000250}.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Mesodermal Commitment Pathway;alk in cardiac myocytes;BMP receptor signaling (Consensus)

Recessive Scores

• pRec: 0.358

Intolerance Scores

• loftool: 0.715
• rvis_EVS: -0.68
• rvis_percentile_EVS: 15.36

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.661

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: chrd
• Affected structure: primordial germ cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: skeletal system development;osteoblast differentiation;gastrulation with mouth forming second;mesoderm formation;positive regulation of mesenchymal cell proliferation;BMP signaling pathway involved in spinal cord dorsal/ventral patterning;negative regulation of cell migration;negative regulation of BMP signaling pathway;forebrain development;floor plate development;negative regulation of osteoblast differentiation;positive regulation of cell adhesion
• Cellular component: extracellular space
• Molecular function: protein binding;heparin binding;cytokine binding;syndecan binding