CGRRF1

cell growth regulator with ring finger domain 1, the group of Ring finger proteins

Basic information

Region (hg38): 14:54509812-54539292

Links

ENSG00000100532 ∙ NCBI:10668 ∙ OMIM:606138 ∙ HGNC:15528 ∙ Uniprot:Q99675 ∙ 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 CGRRF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGRRF1 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					1	1
missense			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	2

Variants in CGRRF1

This is a list of pathogenic ClinVar variants found in the CGRRF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-54509978-G-T		not specified	Uncertain significance (Jan 23, 2024)
14-54522509-A-G		not specified	Uncertain significance (Nov 12, 2021)
14-54530061-T-G		not specified	Uncertain significance (Sep 16, 2021)
14-54530082-A-C		not specified	Uncertain significance (May 06, 2022)
14-54530088-T-C		not specified	Uncertain significance (Jan 31, 2023)
14-54530143-G-T		not specified	Uncertain significance (Feb 17, 2023)
14-54530185-A-T		not specified	Uncertain significance (Jan 16, 2024)
14-54531033-C-T			Benign (Dec 31, 2019)
14-54537803-G-A		not specified	Uncertain significance (Nov 13, 2023)
14-54538084-A-G		not specified	Uncertain significance (Mar 19, 2024)
14-54538133-A-G		not specified	Uncertain significance (Mar 23, 2022)
14-54538184-C-T		not specified	Uncertain significance (Apr 06, 2024)
14-54538240-C-T		not specified	Uncertain significance (Jul 25, 2023)
14-54538296-G-T		not specified	Uncertain significance (Dec 08, 2023)
14-54538371-G-A			Benign (Jun 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGRRF1	protein_coding	protein_coding	ENST00000216420	6	29038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00732	0.978	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.223	157	165	0.951	0.00000748	2178
Missense in Polyphen		46	50.952	0.9028		694
Synonymous	0.535	58	63.4	0.915	0.00000292	601
Loss of Function	2.14	6	14.9	0.402	6.24e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000410	0.000406
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000343	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Able to inhibit growth in several cell lines. {ECO:0000250|UniProtKB:P97587}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.646
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.0519
• hipred: N
• hipred_score: 0.350
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cgrrf1

Gene ontology

• Biological process: cell cycle arrest;negative regulation of cell population proliferation
• Cellular component: nucleoplasm;endoplasmic reticulum;intracellular membrane-bounded organelle
• Molecular function: metal ion binding