CRTAC1

protein-coding

cartilage acidic protein 1

Gene summary

This gene encodes a glycosylated extracellular matrix protein that is found in the interterritorial matrix of articular deep zone cartilage. This protein is used as a marker to distinguish chondrocytes from osteoblasts and mesenchymal stem cells in culture. The presence of FG-GAP motifs and an RGD integrin-binding motif suggests that this protein may be involved in cell-cell or cell-matrix interactions. Copy number alterations in this gene have been observed in neurofibromatosis type 1-associated glomus tumors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

MANE transcript

NM_018058.7

Inheritance

—

ClinVar variants

U:118B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr10:97,865,000-98,030,828

External References & Databases

Ensembl (ENSG00000095713)

Transcript & Mutation Effects

hg38 • Region Span ~165.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CRTAC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018058.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			8 clinvar	1 clinvar		9
missense			103 clinvar	3 clinvar		106
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	118	4	0	122

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018058.7	RefSeq	NP_060528.3	15	MANE Select
ENST00000370597.8	Ensembl	ENSP00000359629.3	15	MANE Select
NM_001206528.3	RefSeq	NP_001193457.1	15	Standard
ENST00000309155.3	Ensembl	ENSP00000310810.3	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

axonal fasciculation
olfactory bulb development
negative regulation of receptor binding

Molecular Function

calcium ion binding
protein binding

Cellular Component

growth cone
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370597
Coding exons: 15
Length: 165829
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125748
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	374	444	0.842	0.0000296	4286
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00027	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.436
RVIS EVS: -0.77
RVIS percentile EVS: 13.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.313

Gene Damage Prediction

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