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.

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.

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	3	5
missense			85	5	1	91
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	86	7	5

Variants in CHRD

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

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

Position	Type	Phenotype	Significance	ClinVar
3-184380361-G-C		not specified	Uncertain significance (Oct 20, 2024)
3-184380386-C-T		not specified	Uncertain significance (Jun 07, 2024)
3-184380394-G-T		not specified	Uncertain significance (Feb 21, 2024)
3-184380400-G-A		not specified	Uncertain significance (Sep 26, 2023)
3-184380424-A-C		not specified	Uncertain significance (Nov 09, 2021)
3-184380451-G-A		not specified	Uncertain significance (Apr 22, 2022)
3-184380464-CA-C			Uncertain significance (Jan 01, 2019)
3-184380784-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-184381247-C-G		not specified	Uncertain significance (Dec 19, 2022)
3-184381505-G-T		not specified	Uncertain significance (Oct 09, 2024)
3-184381529-T-A		not specified	Uncertain significance (May 26, 2024)
3-184381574-A-G		not specified	Uncertain significance (Aug 17, 2022)
3-184381616-G-C		not specified	Uncertain significance (Feb 01, 2023)
3-184381716-A-T		not specified	Uncertain significance (Oct 13, 2023)
3-184381740-C-T		not specified	Uncertain significance (Feb 19, 2025)
3-184381795-C-G			Likely benign (Jul 01, 2022)
3-184381937-G-T		not specified	Uncertain significance (Apr 12, 2022)
3-184382405-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-184382417-G-A		not specified	Uncertain significance (Feb 01, 2025)
3-184382417-G-T		not specified	Uncertain significance (Jun 04, 2024)
3-184382428-C-G		not specified	Uncertain significance (Aug 27, 2024)
3-184382440-G-A		not specified	Uncertain significance (Feb 19, 2025)
3-184382441-C-A		not specified	Uncertain significance (Jun 02, 2023)
3-184382509-C-G		not specified	Uncertain significance (Jul 12, 2022)
3-184382509-C-T		not specified	Uncertain significance (May 08, 2023)

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
0.0000379	1.00	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

Haploinsufficiency Scores

• pHI: 0.261
• hipred: Y
• hipred_score: 0.639
• ghis: 0.610

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

Mouse Genome Informatics

• Gene name: Chrd
• Phenotype: vision/eye 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); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; taste/olfaction phenotype

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