PLLP

plasmolipin, the group of MARVEL domain containing|Tetraspan junctional complex superfamily

Basic information

Region (hg38): 16:57248547-57284672

Previous symbols: [ "TM4SF11" ]

Links

ENSG00000102934 ∙ NCBI:51090 ∙ OMIM:600340 ∙ HGNC:18553 ∙ Uniprot:Q9Y342 ∙ 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 PLLP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLLP 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in PLLP

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

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

Position	Type	Phenotype	Significance	ClinVar
16-57248556-A-T			Uncertain significance (Jul 10, 2023)
16-57248557-C-A			Uncertain significance (Jan 19, 2024)
16-57248570-T-G		Retinitis pigmentosa with or without situs inversus	Uncertain significance (Nov 08, 2022)
16-57248573-A-G			Uncertain significance (Oct 24, 2022)
16-57248574-C-T		Retinal dystrophy	Likely benign (Oct 01, 2023)
16-57248574-C-CAAGTA			Pathogenic (Aug 17, 2021)
16-57248602-G-A			Uncertain significance (Jun 19, 2022)
16-57248618-T-C			Uncertain significance (Nov 08, 2022)
16-57248625-AC-A			Pathogenic (Jul 11, 2022)
16-57248626-C-A			Uncertain significance (Feb 18, 2020)
16-57248642-A-G			Uncertain significance (Jun 13, 2022)
16-57248643-C-A			Pathogenic (Oct 22, 2023)
16-57248643-C-T			Likely benign (Oct 17, 2023)
16-57248644-G-A		Retinal dystrophy • ARL2BP-related disorder • Retinitis pigmentosa with or without situs inversus	Pathogenic (Oct 03, 2023)
16-57248644-G-T		Retinitis pigmentosa with or without situs inversus • Autosomal recessive retinitis pigmentosa	Pathogenic (Aug 08, 2018)
16-57248648-G-A			Uncertain significance (Nov 22, 2022)
16-57248658-A-C			Likely benign (Feb 22, 2022)
16-57248658-A-G			Likely benign (Aug 18, 2023)
16-57248662-C-T			Likely benign (Oct 13, 2023)
16-57249764-C-T			Uncertain significance (Jun 20, 2022)
16-57249789-T-C		Retinal dystrophy	Uncertain significance (Jan 01, 2020)
16-57249794-G-T			Pathogenic (Jun 01, 2023)
16-57249805-G-A			Likely benign (Feb 10, 2023)
16-57249809-C-T		Retinal dystrophy • Inborn genetic diseases	Uncertain significance (Nov 22, 2022)
16-57249810-G-A			Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLLP	protein_coding	protein_coding	ENST00000219207	4	28596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00919	0.823	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.874	84	110	0.765	0.00000677	1142
Missense in Polyphen		26	38.321	0.67847		414
Synonymous	0.400	47	50.6	0.928	0.00000345	385
Loss of Function	1.10	4	7.17	0.558	3.06e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Appears to be involved in myelination. Could also participate in ion transport events as addition of plasmolipin to lipid bilayers induces the formation of ion channels, which are voltage-dependent and K(+)-selective (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.138
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.390
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pllp

Zebrafish Information Network

• Gene name: pllp
• Affected structure: enterocyte
• Phenotype tag: abnormal
• Phenotype quality: mislocalised radially

Gene ontology

• Biological process: ion transport;response to wounding;myelination
• Cellular component: integral component of membrane;compact myelin;membrane raft
• Molecular function: protein binding;structural constituent of myelin sheath