PLSCR4

phospholipid scramblase 4, the group of Phospholipid scramblases

Basic information

Region (hg38): 3:146192334-146251179

Links

ENSG00000114698 ∙ NCBI:57088 ∙ OMIM:607612 ∙ HGNC:16497 ∙ Uniprot:Q9NRQ2 ∙ 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 PLSCR4 gene.

• Inborn genetic diseases (12 variants)
• Sensorineural hearing loss disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLSCR4 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			13			13
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	0	0

Variants in PLSCR4

This is a list of pathogenic ClinVar variants found in the PLSCR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-146195255-T-C		not specified	Uncertain significance (Jan 02, 2024)
3-146196666-G-A		not specified	Uncertain significance (Aug 30, 2022)
3-146196703-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-146196750-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-146196762-A-G		not specified	Uncertain significance (Aug 17, 2022)
3-146199841-C-A		not specified	Uncertain significance (Aug 04, 2023)
3-146199844-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-146199863-G-T		not specified	Uncertain significance (Dec 20, 2023)
3-146199865-C-T		not specified	Uncertain significance (Jun 13, 2023)
3-146199893-T-C		not specified	Uncertain significance (May 24, 2023)
3-146199917-A-C		not specified	Uncertain significance (Nov 20, 2023)
3-146200034-T-C		not specified	Uncertain significance (Jan 16, 2024)
3-146201067-A-G		not specified	Uncertain significance (Dec 14, 2022)
3-146206564-T-C		not specified	Uncertain significance (Aug 02, 2023)
3-146206579-G-A		Sensorineural hearing loss disorder	Uncertain significance (Sep 30, 2020)
3-146206617-T-C		not specified	Uncertain significance (Apr 04, 2023)
3-146206635-C-A		not specified	Uncertain significance (May 09, 2022)
3-146206740-G-A		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLSCR4	protein_coding	protein_coding	ENST00000354952	8	58841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000190	0.697	125637	0	110	125747	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.431	170	187	0.911	0.00000943	2165
Missense in Polyphen		51	58.726	0.86843		687
Synonymous	-0.367	64	60.4	1.06	0.00000298	615
Loss of Function	1.12	11	15.8	0.697	7.51e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00123
Ashkenazi Jewish	0.000310	0.000298
East Asian	0.000637	0.000598
Finnish	0.000534	0.000508
European (Non-Finnish)	0.000330	0.000308
Middle Eastern	0.000637	0.000598
South Asian	0.000262	0.000261
Other	0.00104	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May mediate accelerated ATP-independent bidirectional transbilayer migration of phospholipids upon binding calcium ions that results in a loss of phospholipid asymmetry in the plasma membrane. May play a central role in the initiation of fibrin clot formation, in the activation of mast cells and in the recognition of apoptotic and injured cells by the reticuloendothelial system.

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.910
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.131
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plscr4

Gene ontology

• Biological process: plasma membrane phospholipid scrambling;cellular response to lipopolysaccharide
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: calcium ion binding;protein binding;SH3 domain binding;phospholipid scramblase activity;enzyme binding;CD4 receptor binding