PLSCR5

phospholipid scramblase family member 5, the group of Phospholipid scramblases

Basic information

Region (hg38): 3:146576555-146605346

Links

ENSG00000231213 ∙ NCBI:389158 ∙ ∙ HGNC:19952 ∙ Uniprot:A0PG75 ∙ 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 PLSCR5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLSCR5 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PLSCR5

This is a list of pathogenic ClinVar variants found in the PLSCR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-146589669-C-T		not specified	Uncertain significance (Apr 01, 2024)
3-146589673-T-C		not specified	Uncertain significance (Aug 19, 2021)
3-146589693-A-T		not specified	Uncertain significance (Aug 30, 2022)
3-146589697-C-T		not specified	Uncertain significance (Sep 14, 2022)
3-146589702-T-C		not specified	Uncertain significance (Apr 24, 2024)
3-146589714-T-C		not specified	Uncertain significance (Sep 20, 2024)
3-146589732-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-146589799-C-G		not specified	Uncertain significance (May 05, 2023)
3-146589807-G-T		not specified	Uncertain significance (Oct 17, 2024)
3-146591730-A-G		not specified	Uncertain significance (Feb 07, 2025)
3-146591752-T-G		not specified	Uncertain significance (Aug 28, 2023)
3-146591775-A-C		not specified	Uncertain significance (Sep 27, 2021)
3-146591784-T-C		not specified	Uncertain significance (Oct 12, 2021)
3-146593976-T-C		not specified	Uncertain significance (Jan 27, 2025)
3-146594044-C-A		not specified	Uncertain significance (Apr 25, 2023)
3-146594044-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-146594045-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-146594057-T-A		not specified	Uncertain significance (Apr 06, 2022)
3-146594102-T-G		not specified	Uncertain significance (Mar 29, 2022)
3-146600412-T-C		not specified	Uncertain significance (Dec 23, 2024)
3-146600424-G-A		not specified	Uncertain significance (Dec 10, 2024)
3-146600461-C-A		not specified	Uncertain significance (Jul 06, 2021)
3-146600463-T-A		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLSCR5	protein_coding	protein_coding	ENST00000443512	7	29662

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.08e-10	0.0466	124229	1	396	124626	0.00159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.17	166	129	1.29	0.00000620	1766
Missense in Polyphen		69	52.105	1.3243		702
Synonymous	-2.29	66	46.2	1.43	0.00000230	519
Loss of Function	-0.279	14	12.9	1.08	6.32e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00183
Ashkenazi Jewish	0.000405	0.000398
East Asian	0.00301	0.00301
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000817	0.000814
Middle Eastern	0.00301	0.00301
South Asian	0.00588	0.00590
Other	0.00232	0.00232

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.443

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: Plscr5

Gene ontology

• Biological process: plasma membrane phospholipid scrambling
• Cellular component: plasma membrane
• Molecular function: phospholipid scramblase activity