GYPA

glycophorin A (MNS blood group), the group of Blood group antigens|CD molecules

Basic information

Region (hg38): 4:144109302-144140751

Previous symbols: [ "MNS" ]

Links

ENSG00000170180 ∙ NCBI:2993 ∙ OMIM:617922 ∙ HGNC:4702 ∙ Uniprot:P02724 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, MN locus; Blood group, Erik	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	275842; 7040988; 7052193; 8245024

ClinVar

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

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GYPA 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			6	2		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	0

Variants in GYPA

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

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

Position	Type	Phenotype	Significance	ClinVar
4-144114692-G-T		not specified	Uncertain significance (Nov 08, 2022)
4-144114760-G-A		not specified	Uncertain significance (Jan 23, 2024)
4-144114761-G-A		not specified	Likely benign (Feb 23, 2023)
4-144116864-C-A		not specified	Uncertain significance (Jun 21, 2023)
4-144116868-G-T		not specified	Uncertain significance (Aug 22, 2023)
4-144116874-C-T		not specified	Uncertain significance (Mar 02, 2023)
4-144118734-G-A		not specified	Likely benign (Mar 17, 2023)
4-144119686-C-T		BLOOD GROUP ERIK	Pathogenic (Dec 05, 1993)
4-144119713-T-C		not specified	Uncertain significance (Aug 17, 2022)
4-144119749-G-T		not specified	Uncertain significance (Jan 07, 2022)
4-144120546-A-G		not specified	Likely benign (Nov 22, 2023)
4-144120558-G-T		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GYPA	protein_coding	protein_coding	ENST00000360771	7	31448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00108	0.842	125659	0	4	125663	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.550	94	80.2	1.17	0.00000418	928
Missense in Polyphen		28	25.834	1.0839		325
Synonymous	-0.0271	28	27.8	1.01	0.00000153	297
Loss of Function	1.22	6	10.2	0.588	5.16e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycophorin A is the major intrinsic membrane protein of the erythrocyte. The N-terminal glycosylated segment, which lies outside the erythrocyte membrane, has MN blood group receptors. Appears to be important for the function of SLC4A1 and is required for high activity of SLC4A1. May be involved in translocation of SLC4A1 to the plasma membrane. Is a receptor for influenza virus. Is a receptor for Plasmodium falciparum erythrocyte-binding antigen 175 (EBA-175); binding of EBA-175 is dependent on sialic acid residues of the O-linked glycans. Appears to be a receptor for Hepatitis A virus (HAV). {ECO:0000269|PubMed:10926825, ECO:0000269|PubMed:12813056, ECO:0000269|PubMed:14604989, ECO:0000269|PubMed:15331714, ECO:0000269|PubMed:19438409, ECO:0000269|PubMed:8009226}.
• Pathway: Malaria - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Hematopoietic Stem Cell Differentiation;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.0726
• hipred: N
• hipred_score: 0.146
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gypa
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: viral entry into host cell;leukocyte migration
• Cellular component: plasma membrane;membrane;integral component of membrane
• Molecular function: virus receptor activity;protein binding;identical protein binding