CHRDL2

chordin like 2, the group of Chordin family|MicroRNA protein coding host genes

Basic information

Region (hg38): 11:74696429-74731426

Links

ENSG00000054938 ∙ NCBI:25884 ∙ OMIM:613127 ∙ HGNC:24168 ∙ Uniprot:Q6WN34 ∙ 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 CHRDL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRDL2 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			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in CHRDL2

This is a list of pathogenic ClinVar variants found in the CHRDL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74696520-T-A		not specified	Uncertain significance (May 11, 2022)
11-74696574-C-T		not specified	Uncertain significance (May 13, 2024)
11-74697221-G-A		not specified	Uncertain significance (Dec 19, 2023)
11-74702829-T-C		not specified	Uncertain significance (May 31, 2023)
11-74702832-G-A		not specified	Uncertain significance (Mar 31, 2022)
11-74702845-C-T		not specified	Uncertain significance (Dec 07, 2021)
11-74702896-C-T		not specified	Uncertain significance (May 23, 2023)
11-74702905-G-A		not specified	Uncertain significance (Feb 13, 2024)
11-74702919-G-A		not specified	Uncertain significance (Jun 17, 2024)
11-74702928-G-C		not specified	Uncertain significance (Dec 13, 2021)
11-74703349-C-T		not specified	Likely benign (Jun 21, 2022)
11-74703379-C-T		not specified	Uncertain significance (Dec 02, 2022)
11-74703403-T-C		not specified	Uncertain significance (Jun 29, 2022)
11-74703481-T-C		not specified	Uncertain significance (May 09, 2023)
11-74704495-G-A		not specified	Uncertain significance (Dec 19, 2023)
11-74704576-C-T		not specified	Uncertain significance (Dec 21, 2022)
11-74704593-G-A		not specified	Uncertain significance (Jul 15, 2021)
11-74704648-G-A		not specified	Likely benign (Oct 27, 2023)
11-74706500-G-A		not specified	Uncertain significance (May 30, 2023)
11-74708311-C-T		not specified	Uncertain significance (Apr 27, 2024)
11-74708377-C-T		not specified	Uncertain significance (Oct 18, 2021)
11-74710878-G-A		not specified	Uncertain significance (Mar 31, 2024)
11-74713398-G-T		not specified	Uncertain significance (Apr 08, 2024)
11-74713476-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-74718736-C-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRDL2	protein_coding	protein_coding	ENST00000263671	12	34957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000159	0.965	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	215	268	0.804	0.0000156	2907
Missense in Polyphen		80	97.74	0.8185		1086
Synonymous	-0.153	109	107	1.02	0.00000677	879
Loss of Function	1.97	13	23.3	0.559	0.00000101	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00133
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May inhibit BMPs activity by blocking their interaction with their receptors. Has a negative regulator effect on the cartilage formation/regeneration from immature mesenchymal cells, by preventing or reducing the rate of matrix accumulation (By similarity). Implicated in tumor angiogenesis. May play a role during myoblast and osteoblast differentiation, and maturation. {ECO:0000250, ECO:0000269|PubMed:12853144, ECO:0000269|PubMed:15094188}.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.791
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrdl2

Zebrafish Information Network

• Gene name: chrdl2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: truncated

Gene ontology

• Biological process: ossification;cell differentiation;cartilage development
• Cellular component: extracellular space;cytoplasm