PLD5

phospholipase D family member 5, the group of Phospholipases

Basic information

Region (hg38): 1:242082986-242524697

Links

ENSG00000180287 ∙ NCBI:200150 ∙ ∙ HGNC:26879 ∙ Uniprot:Q8N7P1 ∙ 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 PLD5 gene.

• not_specified (35 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLD5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001372062.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	2	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLD5	protein_coding	protein_coding	ENST00000536534	10	441711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0307	0.969	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	207	280	0.740	0.0000146	3533
Missense in Polyphen		47	90.487	0.51941		1138
Synonymous	0.221	109	112	0.973	0.00000660	972
Loss of Function	3.46	8	27.6	0.290	0.00000141	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000873	0.0000873
Ashkenazi Jewish	0.000499	0.000496
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000980	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000675	0.0000653
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0898

Intolerance Scores

• loftool: 0.570
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.597
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.374

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pld5
• Phenotype: normal phenotype; skeleton phenotype; growth/size/body region phenotype

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: catalytic activity