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.

• not_specified (51 variants)

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. These statistics are base on transcript: NM_001278473.3. 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			4
missense			48	2		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	2	0

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