PLD5

phospholipase D family member 5, the group of Phospholipases

Basic information

Region (hg38): 1:242082985-242524697

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.

• Inborn genetic diseases (14 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.

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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in PLD5

This is a list of pathogenic ClinVar variants found in the PLD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-242089859-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-242089886-C-T		not specified	Likely benign (Dec 28, 2022)
1-242090023-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-242090029-T-C		not specified	Uncertain significance (Aug 17, 2022)
1-242107774-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-242107807-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-242113930-C-G		not specified	Uncertain significance (Jul 31, 2023)
1-242113951-T-C		not specified	Uncertain significance (Apr 08, 2022)
1-242220086-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-242265387-A-G		not specified	Uncertain significance (Sep 20, 2023)
1-242265441-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-242288414-T-G		not specified	Uncertain significance (Mar 08, 2024)
1-242288423-T-C		not specified	Uncertain significance (Apr 13, 2022)
1-242348152-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-242348167-C-G		not specified	Uncertain significance (Mar 07, 2024)
1-242348205-C-A		not specified	Uncertain significance (Dec 20, 2021)
1-242348212-G-A			Likely benign (Dec 01, 2022)
1-242524140-T-G		not specified	Uncertain significance (Feb 27, 2024)
1-242524204-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-242524232-C-G		not specified	Uncertain significance (Apr 07, 2023)

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