CD52

CD52 molecule, the group of CD molecules

Basic information

Region (hg38): 1:26317957-26320523

Previous symbols: [ "CDW52" ]

Links

ENSG00000169442 ∙ NCBI:1043 ∙ OMIM:114280 ∙ HGNC:1804 ∙ Uniprot:P31358 ∙ 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 CD52 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD52 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
missense			3	1	2	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	2	2

Variants in CD52

This is a list of pathogenic ClinVar variants found in the CD52 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26318029-C-T		CD52-related disorder	Likely benign (Mar 18, 2019)
1-26318060-G-C		not specified	Uncertain significance (Jan 23, 2023)
1-26318066-G-C		not specified	Uncertain significance (Jul 14, 2021)
1-26320235-A-G		CD52-related disorder	Benign (Oct 16, 2019)
1-26320239-A-G		CD52-related disorder	Benign (Sep 24, 2019)
1-26320264-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-26320292-G-A		not specified	Likely benign (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD52	protein_coding	protein_coding	ENST00000374213	2	2567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.403	0.480	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	27	35.6	0.758	0.00000193	400
Missense in Polyphen		2	2.4551	0.81464		19
Synonymous	0.596	11	13.8	0.796	8.42e-7	120
Loss of Function	0.965	0	1.08	0.00	4.61e-8	12

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in carrying and orienting carbohydrate, as well as having a more specific role.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.375
• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.92

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd52
• Phenotype: normal phenotype

Gene ontology

• Biological process: positive regulation of cytosolic calcium ion concentration;respiratory burst
• Cellular component: extracellular region;plasma membrane;membrane;anchored component of membrane;intrinsic component of plasma membrane;sperm midpiece