CGREF1

cell growth regulator with EF-hand domain 1, the group of EF-hand domain containing

Basic information

Region (hg38): 2:27098889-27119128

Links

ENSG00000138028 ∙ NCBI:10669 ∙ OMIM:606137 ∙ HGNC:16962 ∙ Uniprot:Q99674 ∙ 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 CGREF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CGREF1 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		2	4
Total	0	0	12	1	2

Variants in CGREF1

This is a list of pathogenic ClinVar variants found in the CGREF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27099274-G-C		Essential fructosuria	Uncertain significance (Jan 12, 2018)
2-27099289-G-A		Essential fructosuria	Uncertain significance (Jan 12, 2018)
2-27099411-G-A			Benign (Jul 15, 2018)
2-27099444-TGAG-T		Essential fructosuria	Uncertain significance (Jun 14, 2016)
2-27099449-A-T		not specified	Uncertain significance (Oct 04, 2022)
2-27099453-C-T		Essential fructosuria	Uncertain significance (Apr 27, 2017)
2-27099454-G-A		Essential fructosuria • not specified	Uncertain significance (Apr 12, 2022)
2-27099464-T-G		Essential fructosuria	Uncertain significance (Jan 13, 2018)
2-27099514-G-A		not specified	Uncertain significance (Jan 06, 2023)
2-27099556-G-A		Essential fructosuria	Conflicting classifications of pathogenicity (Jun 08, 2018)
2-27099582-G-C		Essential fructosuria • KHK-related disorder	Benign (Apr 27, 2017)
2-27099670-A-G		KHK-related disorder	Likely benign (May 05, 2020)
2-27099671-G-A		Essential fructosuria	Uncertain significance (Jan 12, 2018)
2-27099673-G-A		Essential fructosuria	Uncertain significance (Jan 12, 2018)
2-27099679-G-A		Essential fructosuria	Uncertain significance (Jan 13, 2018)
2-27099719-G-A		Essential fructosuria	Uncertain significance (Jan 12, 2018)
2-27099732-C-A		Essential fructosuria	Benign (Jul 15, 2018)
2-27099738-T-C		Essential fructosuria	Likely benign (Jan 13, 2018)
2-27099761-C-T		Essential fructosuria	Uncertain significance (Jan 13, 2018)
2-27099768-TCA-T		Essential fructosuria	Likely benign (Jun 14, 2016)
2-27099777-A-G		Essential fructosuria	Likely benign (Jan 13, 2018)
2-27099778-T-C		Essential fructosuria	Uncertain significance (Jan 13, 2018)
2-27099799-C-T		Essential fructosuria	Uncertain significance (Jan 13, 2018)
2-27099802-C-T		Essential fructosuria	Uncertain significance (Jan 12, 2018)
2-27099803-G-A		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CGREF1	protein_coding	protein_coding	ENST00000402394	5	20239

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.74e-8	0.0653	125536	0	212	125748	0.000843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	131	169	0.775	0.00000820	2030
Missense in Polyphen		41	43.912	0.93369		564
Synonymous	-0.330	76	72.4	1.05	0.00000380	680
Loss of Function	-0.711	10	7.85	1.27	3.33e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00354	0.00354
Finnish	0.00110	0.00106
European (Non-Finnish)	0.000581	0.000580
Middle Eastern	0.00354	0.00354
South Asian	0.00131	0.00131
Other	0.00123	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates cell-cell adhesion in a calcium-dependent manner (By similarity). Able to inhibit growth in several cell lines. {ECO:0000250}.

Intolerance Scores

• loftool: 0.700
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.8

Haploinsufficiency Scores

• pHI: 0.0585
• hipred: N
• hipred_score: 0.153
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00179

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cgref1

Gene ontology

• Biological process: cell cycle arrest;cell adhesion;negative regulation of cell population proliferation
• Cellular component: extracellular region
• Molecular function: calcium ion binding