GYPB

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

Basic information

Region (hg38): 4:143996104-144019380

Previous symbols: [ "MNS" ]

Links

ENSG00000250361 ∙ NCBI:2994 ∙ OMIM:617923 ∙ HGNC:4703 ∙ Uniprot:P06028 ∙ 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, Ss	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	3818169; 3456608; 2823938; 3477806

ClinVar

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

Variants pathogenicity by type

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

Variants in GYPB

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

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

Position	Type	Phenotype	Significance	ClinVar
4-143997550-C-T			Likely benign (Oct 01, 2024)
4-143997559-C-C			Benign (Aug 01, 2018)
4-143997560-T-C			Likely benign (Oct 01, 2024)
4-143997603-A-C		not specified	Uncertain significance (Jun 11, 2021)
4-143997622-A-G		not specified	Uncertain significance (Nov 15, 2024)
4-143999413-G-C		BLOOD GROUP, Ss	association (-)
4-144001187-T-C		not specified	Uncertain significance (Aug 12, 2024)
4-144001239-G-A		not specified	Uncertain significance (Oct 18, 2021)
4-144001245-C-T		not specified	Uncertain significance (Jan 10, 2022)
4-144001260-T-G		not specified	Uncertain significance (Oct 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GYPB	protein_coding	protein_coding	ENST00000502664	5	144588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000838	0.337	125630	0	6	125636	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	68	47.6	1.43	0.00000250	552
Missense in Polyphen		12	8.2451	1.4554		96
Synonymous	-0.816	20	15.9	1.26	7.94e-7	183
Loss of Function	-0.0717	6	5.81	1.03	2.46e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000950	0.0000921
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a minor sialoglycoprotein in erythrocyte membranes.
• Pathway: Malaria - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Intolerance Scores

• rvis_EVS: 1.68
• rvis_percentile_EVS: 96.36

Haploinsufficiency Scores

• pHI: 8.75
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 1.03e-7

Gene Damage Prediction

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

Gene ontology

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