GYPC

glycophorin C (Gerbich blood group), the group of Blood group antigens|CD molecules

Basic information

Region (hg38): 2:126656132-126696667

Links

ENSG00000136732 ∙ NCBI:2995 ∙ OMIM:110750 ∙ HGNC:4704 ∙ Uniprot:P04921 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary elliptocytosis (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Gerbich; Blood group, Webb; Blood group, Duch	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	5011657; 7095818; 3539763; 1991173; 1719701; 1413665; 8157284; 11719395; 12469115

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GYPC gene.

• not provided (18 variants)
• Blood group, Gerbich system (12 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GYPC 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	2
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding			1		7	8
Total	0	0	21	1	9

Variants in GYPC

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

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

Position	Type	Phenotype	Significance	ClinVar
2-126656286-A-G		Blood group, Gerbich system	Affects (May 01, 1991)
2-126656303-C-T		Blood group, Gerbich system	Affects (Jan 01, 1992)
2-126656307-G-A		Blood group, Gerbich system	Uncertain significance (Jul 16, 2023)
2-126656309-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-126690187-G-A			Benign (Nov 12, 2018)
2-126690251-ACAGAGCCTGATCCGGGGATGGCCTCTGCCTCCACCACAATGCATACTACCACCATTG-A		Blood group, Gerbich system	Affects (Feb 01, 1991)
2-126690264-C-T		GYPC-related disorder	Benign (Aug 09, 2019)
2-126690265-G-A			Likely benign (Dec 01, 2022)
2-126693838-C-T			Uncertain significance (Apr 14, 2020)
2-126693860-ACAGAGCCTGATCCAGGGATGTCTGGATGGCCGGATGGCAGAATGGAGACCTCCACCCCCACCATAATGGACATTGTCGTCATTG-A		Glycophorin c, gerbich variant • Malaria, resistance to	Pathogenic; protective (Jan 01, 2003)
2-126693861-C-T			Uncertain significance (Nov 22, 2021)
2-126693866-C-A		Blood group, Gerbich system	Uncertain significance (Mar 28, 2023)
2-126693891-C-G		Blood group, Gerbich system	Uncertain significance (Mar 31, 2023)
2-126693905-G-A			Uncertain significance (Jan 24, 2023)
2-126693907-G-C		Blood group, Gerbich system • not specified	Uncertain significance (Dec 13, 2023)
2-126693915-C-T			Uncertain significance (Jan 05, 2022)
2-126693924-T-A		Blood group, Gerbich system • not specified	Uncertain significance (Dec 27, 2023)
2-126693929-G-A		not specified	Uncertain significance (Jun 27, 2022)
2-126693936-T-C		not specified	Likely benign (Dec 08, 2023)
2-126693955-C-G		GYPC-related disorder	Benign (Nov 14, 2019)
2-126695682-GT-G			Benign (Nov 12, 2018)
2-126695685-A-C			Benign (Nov 12, 2018)
2-126695725-C-T			Benign (Nov 12, 2018)
2-126695810-C-T			Benign (Nov 12, 2018)
2-126695903-G-A			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GYPC	protein_coding	protein_coding	ENST00000259254	4	40738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.113	0.787	125728	0	6	125734	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.30	107	75.2	1.42	0.00000430	829
Missense in Polyphen		26	20.196	1.2874		253
Synonymous	-1.34	38	28.8	1.32	0.00000180	252
Loss of Function	1.29	2	5.18	0.386	2.24e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a minor sialoglycoprotein in human erythrocyte membranes. The blood group Gerbich antigens and receptors for Plasmodium falciparum merozoites are most likely located within the extracellular domain. Glycophorin-C plays an important role in regulating the stability of red cells.
• Pathway: Malaria - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.821
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.0349
• hipred: N
• hipred_score: 0.213
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.491

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gypc

Gene ontology

• Biological process: leukocyte migration
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;extrinsic component of plasma membrane;cortical cytoskeleton
• Molecular function: protein binding