CRCT1

cysteine rich C-terminal 1

Basic information

Region (hg38): 1:152514481-152516008

Previous symbols: [ "C1orf42" ]

Links

ENSG00000169509 ∙ NCBI:54544 ∙ OMIM:617426 ∙ HGNC:29875 ∙ Uniprot:Q9UGL9 ∙ 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 CRCT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRCT1 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CRCT1

This is a list of pathogenic ClinVar variants found in the CRCT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152515409-C-G		not specified	Uncertain significance (Jun 16, 2024)
1-152515463-C-G		not specified	Uncertain significance (Jul 30, 2023)
1-152515499-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-152515504-G-C		not specified	Uncertain significance (Aug 02, 2023)
1-152515547-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-152515649-A-G		not specified	Uncertain significance (Nov 08, 2022)
1-152515650-C-A		not specified	Uncertain significance (Sep 26, 2022)
1-152515676-G-A		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRCT1	protein_coding	protein_coding	ENST00000368790	1	1509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00194	0.306	120497	0	20	120517	0.0000830

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.389	47	55.1	0.853	0.00000359	598
Missense in Polyphen
Synonymous	-0.896	32	26.2	1.22	0.00000206	206
Loss of Function	-1.45	3	1.25	2.40	5.39e-8	14

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000330	0.0000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.000980	0.000949
Finnish	0.00	0.00
European (Non-Finnish)	0.0000197	0.0000185
Middle Eastern	0.000980	0.000949
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.432
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crct1

Gene ontology

• Molecular function: protein binding