GLCCI1

glucocorticoid induced 1

Basic information

Region (hg38): 7:7968796-8094272

Links

ENSG00000106415 ∙ NCBI:113263 ∙ OMIM:614283 ∙ HGNC:18713 ∙ Uniprot:Q86VQ1 ∙ 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 GLCCI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLCCI1 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			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	2	0

Variants in GLCCI1

This is a list of pathogenic ClinVar variants found in the GLCCI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-7969363-T-G		not specified	Uncertain significance (Nov 17, 2023)
7-7969451-T-G		not specified	Uncertain significance (Oct 20, 2021)
7-7969462-G-C		not specified	Uncertain significance (Aug 12, 2021)
7-7969466-G-C		not specified	Uncertain significance (Aug 12, 2021)
7-7969474-G-A		not specified	Uncertain significance (Mar 14, 2023)
7-7969475-G-C		not specified	Uncertain significance (Aug 12, 2021)
7-7969477-G-C		not specified	Uncertain significance (Aug 12, 2021)
7-7969480-G-A		not specified	Uncertain significance (May 16, 2022)
7-7969501-T-G		not specified	Uncertain significance (Oct 12, 2022)
7-7969503-C-G		not specified	Uncertain significance (Oct 12, 2022)
7-7969504-G-T		not specified	Uncertain significance (Nov 01, 2022)
7-7969517-G-C		not specified	Uncertain significance (Nov 29, 2023)
7-7969649-C-T			Likely benign (Jun 01, 2022)
7-7969655-G-T		not specified	Uncertain significance (Jan 19, 2022)
7-7969663-A-C		not specified	Uncertain significance (Jun 22, 2021)
7-7969664-G-C		not specified	Uncertain significance (Dec 17, 2023)
7-7969669-T-G		not specified	Uncertain significance (Jun 22, 2021)
7-7969672-A-C		not specified	Uncertain significance (Jun 22, 2021)
7-7969673-G-A		not specified	Uncertain significance (Apr 16, 2024)
7-7969681-C-G		not specified	Uncertain significance (Jul 14, 2022)
7-7969700-C-T		not specified	Uncertain significance (Dec 06, 2021)
7-7969705-G-A		not specified	Uncertain significance (Jun 22, 2021)
7-7969721-C-T		not specified	Uncertain significance (Apr 25, 2023)
7-7969793-C-T		not specified	Uncertain significance (Dec 28, 2023)
7-8003908-C-T		not specified	Likely benign (Jan 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLCCI1	protein_coding	protein_coding	ENST00000223145	8	125478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0590	0.940	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	253	259	0.977	0.0000149	3459
Missense in Polyphen		83	103.1	0.80505		1187
Synonymous	0.404	88	93.0	0.947	0.00000498	1158
Loss of Function	2.98	6	20.6	0.291	0.00000111	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.187
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.272
• hipred: N
• hipred_score: 0.494
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glcci1

Zebrafish Information Network

• Gene name: glcci1a
• Affected structure: pronephric capsular space
• Phenotype tag: abnormal
• Phenotype quality: distended

Gene ontology

• Cellular component: cytoplasm