GYPA
glycophorin A (MNS blood group), the group of Blood group antigens|CD molecules
Basic information
Region (hg38): 4:144109303-144140751
Previous symbols: [ "MNS" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| 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
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 | 11 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 3 | 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) | ||
| 4-144116906-C-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| 4-144116930-A-C | not specified | Uncertain significance (Apr 19, 2024) | ||
| 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:
| 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:
- 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