CRTAC1

cartilage acidic protein 1

Basic information

Region (hg38): 10:97865000-98030828

Links

ENSG00000095713 ∙ NCBI:55118 ∙ OMIM:606276 ∙ HGNC:14882 ∙ Uniprot:Q9NQ79 ∙ 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 CRTAC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRTAC1 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			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in CRTAC1

This is a list of pathogenic ClinVar variants found in the CRTAC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97865567-C-G		not specified	Uncertain significance (Jan 05, 2022)
10-97865607-C-T		not specified	Uncertain significance (Jun 27, 2023)
10-97865652-C-T		not specified	Likely benign (Dec 21, 2022)
10-97865670-C-T		not specified	Likely benign (Feb 01, 2023)
10-97865706-C-T		not specified	Uncertain significance (Jun 27, 2022)
10-97880270-C-T		not specified	Uncertain significance (Apr 19, 2024)
10-97880318-A-G		not specified	Uncertain significance (May 08, 2023)
10-97880342-C-T		not specified	Uncertain significance (Jul 17, 2024)
10-97882797-C-A		not specified	Uncertain significance (Dec 18, 2023)
10-97884241-C-T		not specified	Uncertain significance (Dec 19, 2023)
10-97884243-C-T		not specified	Uncertain significance (Jan 20, 2023)
10-97884244-G-A		not specified	Uncertain significance (Jul 02, 2024)
10-97884262-G-T		not specified	Uncertain significance (Dec 27, 2022)
10-97884294-C-T		not specified	Uncertain significance (Mar 01, 2024)
10-97884295-G-A		not specified	Uncertain significance (Jun 26, 2024)
10-97884302-C-T		not specified	Uncertain significance (Jan 10, 2022)
10-97884321-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-97884349-T-C		not specified	Uncertain significance (Jun 21, 2023)
10-97895296-C-T		not specified	Uncertain significance (Jan 16, 2024)
10-97895299-C-T		not specified	Uncertain significance (Aug 05, 2024)
10-97895896-G-A		not specified	Uncertain significance (May 17, 2023)
10-97895902-C-T		not specified	Uncertain significance (Jun 16, 2022)
10-97895952-A-C		not specified	Uncertain significance (Feb 13, 2024)
10-97895961-C-T		not specified	Uncertain significance (Jun 11, 2024)
10-97895962-C-T		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRTAC1	protein_coding	protein_coding	ENST00000370597	15	165829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.49e-7	0.995	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	374	444	0.842	0.0000296	4286
Missense in Polyphen		109	150.58	0.72388		1379
Synonymous	0.420	178	185	0.961	0.0000132	1340
Loss of Function	2.54	15	30.0	0.500	0.00000159	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000470	0.000468
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000484	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000269	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.436
• rvis_EVS: -0.77
• rvis_percentile_EVS: 13.16

Haploinsufficiency Scores

• pHI: 0.142
• hipred: Y
• hipred_score: 0.589
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.313

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crtac1
• 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); cellular phenotype

Gene ontology

• Biological process: axonal fasciculation;olfactory bulb development;negative regulation of receptor binding
• Cellular component: growth cone;extracellular exosome
• Molecular function: calcium ion binding;protein binding