PALS1

protein associated with LIN7 1, MAGUK p55 family member, the group of Crumbs complex|PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 14:67240713-67336061

Previous symbols: [ "MPP5" ]

Links

ENSG00000072415

∙ NCBI:64398 ∙ OMIM:606958 ∙ HGNC:18669 ∙ Uniprot:Q8N3R9 ∙ 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 PALS1 gene.

not_specified (62 variants)
not_provided (7 variants)
PALS1-related_disorder (4 variants)
Neurodevelopmental_disorder (2 variants)
Cerebral_palsy (1 variants)
Arachnoid_cyst (1 variants)
Abnormal_facial_shape (1 variants)
Atypical_Rett_syndrome (1 variants)
Anxiety (1 variants)
Intellectual_disability (1 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022474.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense	1 clinvar		59 clinvar	9 clinvar	1 clinvar	70
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	63	9	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALS1	protein_coding	protein_coding	ENST00000261681	13	94711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.235	0.765	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	296	372	0.795	0.0000200	4481
Missense in Polyphen		98	141.33	0.69343		1707
Synonymous	-0.969	137	123	1.11	0.00000647	1213
Loss of Function	4.10	8	33.7	0.238	0.00000173	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in tight junctions biogenesis and in the establishment of cell polarity in epithelial cells. May modulate SC6A1/GAT1-mediated GABA uptake by stabilizing the transporter. Required for localization of EZR to the apical membrane of parietal cells and may play a role in the dynamic remodeling of the apical cytoskeleton (By similarity). {ECO:0000250}.;
Pathway: Tight junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);EMT transition in Colorectal Cancer;Tight junction interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

pRec: 0.137

Intolerance Scores

loftool: 0.451
rvis_EVS: 0.47
rvis_percentile_EVS: 78.74

Haploinsufficiency Scores

pHI: 0.974
hipred: Y
hipred_score: 0.708
ghis: 0.482

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mpp5
Phenotype: hematopoietic system phenotype; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype;

Zebrafish Information Network

Gene name: mpp5a
Affected structure: cardiac muscle cell
Phenotype tag: abnormal
Phenotype quality: structure

Gene ontology

Biological process: morphogenesis of an epithelial sheet;peripheral nervous system myelin maintenance;myelin assembly;protein localization to myelin sheath abaxonal region;bicellular tight junction assembly;protein localization to plasma membrane;establishment of epithelial cell polarity
Cellular component: cytoplasm;plasma membrane;cell-cell adherens junction;bicellular tight junction;endomembrane system;protein-containing complex;myelin sheath adaxonal region;lateral loop;Schmidt-Lanterman incisure;extracellular exosome
Molecular function: protein binding;protein domain specific binding