GC

GC vitamin D binding protein

Basic information

Region (hg38): 4:71741695-71804041

Links

ENSG00000145321 ∙ NCBI:2638 ∙ OMIM:139200 ∙ HGNC:4187 ∙ Uniprot:P02774 ∙ 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 GC gene.

• Inborn genetic diseases (14 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GC 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				2	4	6
missense			12	3	2	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	12	5	6

Variants in GC

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

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

Position	Type	Phenotype	Significance	ClinVar
4-71752529-A-C		not specified	Uncertain significance (Dec 18, 2023)
4-71752546-T-G		not specified	Uncertain significance (Oct 20, 2023)
4-71752571-A-G		not specified	Uncertain significance (Feb 10, 2022)
4-71752580-G-A			Benign (Aug 20, 2018)
4-71752593-C-T			Likely benign (Aug 01, 2022)
4-71752606-G-T		GC1/GC2 POLYMORPHISM • Levothyroxine response	Benign; other (Jun 01, 1992)
4-71752617-A-C		GC1/GC2 POLYMORPHISM • Periodontitis	Benign (Apr 20, 2023)
4-71752640-G-T			Benign (Apr 10, 2018)
4-71754414-T-A		not specified	Uncertain significance (Aug 17, 2021)
4-71755091-T-C			Likely benign (Aug 20, 2018)
4-71756727-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-71756884-T-C			Benign (Jul 06, 2018)
4-71756904-T-C		not specified	Uncertain significance (Nov 09, 2021)
4-71758062-C-G		not specified	Uncertain significance (Sep 29, 2023)
4-71758112-A-G		not specified	Uncertain significance (Sep 21, 2023)
4-71763401-T-C			Likely benign (Jun 14, 2018)
4-71763422-C-T			Likely benign (Aug 01, 2022)
4-71763456-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-71763482-T-A		not specified	Uncertain significance (Jul 19, 2023)
4-71763857-T-C		not specified	Uncertain significance (Jan 02, 2024)
4-71763912-A-G			Benign (Jun 14, 2018)
4-71765465-G-A		not specified	Uncertain significance (Jan 18, 2023)
4-71765477-T-C		not specified	Uncertain significance (Nov 19, 2022)
4-71765497-G-A			Benign (Aug 18, 2018)
4-71765507-A-T		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GC	protein_coding	protein_coding	ENST00000504199	13	62349

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-11	0.455	125709	0	36	125745	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.399	231	249	0.929	0.0000118	3204
Missense in Polyphen		57	66.286	0.85991		865
Synonymous	-0.362	100	95.5	1.05	0.00000486	928
Loss of Function	1.22	20	26.8	0.746	0.00000131	365

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000385	0.000385
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000480	0.0000462
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000300	0.000294
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5 alpha for neutrophils in inflammation and macrophage activation. {ECO:0000305|PubMed:16302727}.
• Pathway: Vitamin D Metabolism;Metabolism of lipids;Metabolism;Metabolism of steroids;Vitamin D (calciferol) metabolism;Steroid hormones (Consensus)

Recessive Scores

• pRec: 0.430

Intolerance Scores

• loftool: 0.432
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.146
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gc
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; skeleton phenotype

Gene ontology

• Biological process: vitamin transmembrane transport;vitamin D metabolic process;vitamin transport
• Cellular component: extracellular region;extracellular space;cytosol;lysosomal lumen;extracellular exosome;blood microparticle
• Molecular function: actin binding;vitamin D binding;vitamin transmembrane transporter activity;calcidiol binding