CRTAP

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

Basic information

Region (hg38): 3:33114013-33147773

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 (473 variants)
• not provided (60 variants)
• Osteogenesis imperfecta (20 variants)
• not specified (17 variants)
• Inborn genetic diseases (15 variants)
• Osteogenesis Imperfecta, Recessive (10 variants)
• CRTAP-related condition (2 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.

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			4	94	6	104
missense	1	1	148		3	153
nonsense	7	2				9
start loss		1				1
frameshift	16	3	1			20
inframe indel			4			4
splice donor/acceptor (+/-2bp)	1	4	1			6
splice region	1	1	4	7		13
non coding		1	110	53	43	207
Total	25	12	268	147	52

Highest pathogenic variant AF is 0.0000919

Variants in CRTAP

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

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

Position	Type	Phenotype	Significance	ClinVar
3-33114033-T-G		not specified	Likely benign (May 05, 2017)
3-33114039-C-G		not specified	Likely benign (Sep 18, 2017)
3-33114043-C-T		Osteogenesis imperfecta type 7 • not specified	Conflicting classifications of pathogenicity (Jan 13, 2018)
3-33114079-T-C		Osteogenesis imperfecta type 7	Pathogenic (Nov 14, 2023)
3-33114080-G-A		Osteogenesis imperfecta type 7 • Osteogenesis imperfecta	Pathogenic/Likely pathogenic (Feb 25, 2023)
3-33114081-G-C		Osteogenesis imperfecta type 7	Uncertain significance (Aug 20, 2022)
3-33114083-G-A		Osteogenesis imperfecta type 7	Likely benign (Jan 27, 2024)
3-33114083-GC-G		Osteogenesis imperfecta type 7	Pathogenic (Jan 31, 2024)
3-33114085-C-A		Osteogenesis imperfecta type 7	Uncertain significance (Jan 28, 2022)
3-33114086-G-A		Osteogenesis imperfecta type 7	Likely benign (Feb 16, 2023)
3-33114090-C-A		Osteogenesis imperfecta type 7 • Inborn genetic diseases	Uncertain significance (Sep 12, 2022)
3-33114090-CGCCGGGGG-C		CRTAP-related disorder • Osteogenesis imperfecta type 7	Pathogenic/Likely pathogenic (Nov 21, 2023)
3-33114090-C-CGCCGGGGG		Osteogenesis imperfecta type 7	Pathogenic (Oct 28, 2023)
3-33114093-C-A		Osteogenesis imperfecta • Osteogenesis imperfecta type 7	Conflicting classifications of pathogenicity (Dec 16, 2022)
3-33114093-CG-C		Osteogenesis imperfecta type 7	Pathogenic (Oct 06, 2023)
3-33114093-CGGGGGGCCGCGGCGCT-C		Osteogenesis imperfecta type 7	Pathogenic (Aug 29, 2023)
3-33114093-C-CG		Osteogenesis imperfecta type 7	Pathogenic (May 02, 2023)
3-33114094-G-T		Osteogenesis imperfecta type 7	Uncertain significance (Aug 23, 2022)
3-33114093-C-CGG			Pathogenic (-)
3-33114095-G-C		Osteogenesis imperfecta type 7	Likely benign (Nov 06, 2023)
3-33114095-G-T		Osteogenesis imperfecta type 7	Likely benign (Oct 07, 2021)
3-33114097-G-C		Osteogenesis imperfecta type 7	Uncertain significance (Jun 22, 2022)
3-33114098-G-A		Osteogenesis imperfecta type 7	Likely benign (Jan 17, 2024)
3-33114098-GGCCGCGGC-G		Osteogenesis imperfecta type 7	Pathogenic (Jan 18, 2024)
3-33114100-C-T		Osteogenesis imperfecta type 7 • Osteogenesis imperfecta	Uncertain significance (Aug 14, 2021)

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