GYPE

glycophorin E (MNS blood group), the group of Blood group antigens

Basic information

Region (hg38): 4:143870864-143905563

Links

ENSG00000197465 ∙ NCBI:2996 ∙ OMIM:138590 ∙ HGNC:4705 ∙ Uniprot:P15421 ∙ 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 GYPE gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GYPE 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			9		1	10
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	9	0	2

Variants in GYPE

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

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

Position	Type	Phenotype	Significance	ClinVar
4-143876799-C-G		not specified	Uncertain significance (Apr 20, 2024)
4-143876822-C-T		not specified	Uncertain significance (Apr 06, 2022)
4-143876823-G-A		not specified	Uncertain significance (Aug 17, 2021)
4-143876823-G-C		not specified	Uncertain significance (Apr 05, 2023)
4-143876843-A-G		not specified	Uncertain significance (May 08, 2023)
4-143876846-A-C		not specified	Uncertain significance (Sep 08, 2024)
4-143876851-T-C		not specified	Uncertain significance (Mar 31, 2023)
4-143880437-T-C		not specified	Uncertain significance (Oct 03, 2024)
4-143880455-G-A		not specified	Uncertain significance (Oct 12, 2024)
4-143880509-C-G		not specified	Benign (Mar 28, 2016)
4-143880518-A-C			Benign (Jun 20, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GYPE	protein_coding	protein_coding	ENST00000358615	3	34697

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00369	0.649	125571	0	22	125593	0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.225	45	41.0	1.10	0.00000208	476
Missense in Polyphen		1	1.6013	0.62448		16
Synonymous	-0.752	16	12.6	1.27	6.11e-7	152
Loss of Function	0.546	4	5.37	0.746	2.95e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.000461	0.000458
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a minor sialoglycoprotein in human erythrocyte membranes.

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.351
• hipred: N
• hipred_score: 0.112
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000382

Gene Damage Prediction

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

Gene ontology

• Cellular component: plasma membrane;integral component of plasma membrane