LYPD5

LY6/PLAUR domain containing 5, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 19:43785873-43827206

Links

ENSG00000159871 ∙ NCBI:284348 ∙ OMIM:619618 ∙ HGNC:26397 ∙ Uniprot:Q6UWN5 ∙ 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 LYPD5 gene.

• Inborn genetic diseases (7 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPD5 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			6	1		7
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	1	1

Variants in LYPD5

This is a list of pathogenic ClinVar variants found in the LYPD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43797597-T-C			Benign (Aug 06, 2018)
19-43797661-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-43797691-G-T		not specified	Uncertain significance (Mar 03, 2022)
19-43797710-A-G		not specified	Uncertain significance (Feb 28, 2023)
19-43797763-G-C		not specified	Uncertain significance (Jan 16, 2024)
19-43797791-G-A		not specified	Uncertain significance (Jan 19, 2022)
19-43798457-A-G		not specified	Uncertain significance (Dec 03, 2021)
19-43798469-C-T		not specified	Uncertain significance (Dec 08, 2023)
19-43798475-C-G		not specified	Uncertain significance (Jan 30, 2024)
19-43798554-C-G		not specified	Uncertain significance (Sep 07, 2022)
19-43798557-T-C		not specified	Likely benign (Jun 27, 2022)
19-43798944-C-G		not specified	Uncertain significance (Dec 19, 2023)
19-43798983-G-T		not specified	Uncertain significance (Jan 29, 2024)
19-43799727-C-A		not specified	Uncertain significance (Dec 11, 2023)
19-43799760-G-C		not specified	Uncertain significance (Sep 29, 2023)
19-43802374-T-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYPD5	protein_coding	protein_coding	ENST00000377950	5	31278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000472	0.687	125712	0	32	125744	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.780	119	145	0.818	0.00000702	1589
Missense in Polyphen		30	43.172	0.69489		460
Synonymous	0.950	53	62.6	0.847	0.00000316	524
Loss of Function	0.803	6	8.53	0.703	4.25e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000810
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000289	0.0000264
Middle Eastern	0.000328	0.000326
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Intolerance Scores

• loftool: 0.801
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.180
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lypd5

Gene ontology

• Biological process: cell-matrix adhesion
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: laminin binding