CRTAP

cartilage associated protein, the group of Prolyl 3-hydroxylase family

Basic information

Region (hg38): 3:33114014-33147773

Links

ENSG00000170275 ∙ NCBI:10491 ∙ OMIM:605497 ∙ HGNC:2379 ∙ Uniprot:O75718 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• osteogenesis imperfecta type 7 (Strong), mode of inheritance: AR
• osteogenesis imperfecta type 7 (Strong), mode of inheritance: AR
• osteogenesis imperfecta type 2 (Supportive), mode of inheritance: AD
• osteogenesis imperfecta type 3 (Supportive), mode of inheritance: AD
• osteogenesis imperfecta type 4 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Osteogenesis imperfecta, type VII	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Ophthalmologic	12110406; 17192541; 17055431; 19862557; 21955071; 21964860; 23613367; 25604815

ClinVar

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

• Osteogenesis_imperfecta_type_7 (458 variants)
• Inborn_genetic_diseases (58 variants)
• not_provided (55 variants)
• Osteogenesis_imperfecta (20 variants)
• not_specified (19 variants)
• CRTAP-related_disorder (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRTAP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006371.5. 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			1	165	3	169
missense	3	1	177	5	3	189
nonsense	16	5	1			22
start loss	1	1				2
frameshift	20	12	2			34
splice donor/acceptor (+/-2bp)	2	7				9
Total	42	26	181	170	6

Highest pathogenic variant AF is 0.000165759

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRTAP	protein_coding	protein_coding	ENST00000320954	7	33795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000554	0.975	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.441	225	207	1.09	0.0000105	2597
Missense in Polyphen		46	44.02	1.045		560
Synonymous	-1.62	104	85.0	1.22	0.00000474	733
Loss of Function	2.00	8	16.8	0.475	8.11e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.000233	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000233	0.000217
South Asian	0.000135	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for efficient 3-hydroxylation of fibrillar collagen prolyl residues. {ECO:0000269|PubMed:17055431}.
• Pathway: Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.459
• ghis: 0.644

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crtap
• Phenotype: growth/size/body region phenotype; skeleton phenotype

Gene ontology

• Biological process: spermatogenesis;peptidyl-proline hydroxylation to 3-hydroxy-L-proline;protein stabilization;chaperone-mediated protein folding;negative regulation of post-translational protein modification
• Cellular component: extracellular space;endoplasmic reticulum;endoplasmic reticulum lumen;protein-containing complex
• Molecular function: protein binding