PALS2

protein associated with LIN7 2, MAGUK p55 family member, the group of PDZ domain containing|Membrane associated guanylate kinases

Basic information

Region (hg38): 7:24573268-24694193

Previous symbols: [ "MPP6" ]

Links

ENSG00000105926 ∙ NCBI:51678 ∙ OMIM:606959 ∙ HGNC:18167 ∙ Uniprot:Q9NZW5 ∙ 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 PALS2 gene.

• not_specified (49 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001303037.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			49			49
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	1	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALS2	protein_coding	protein_coding	ENST00000222644	11	120926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.816	0.184	125730	0	14	125744	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	184	285	0.646	0.0000141	3552
Missense in Polyphen		52	101.29	0.51339		1249
Synonymous	-0.125	100	98.4	1.02	0.00000475	1000
Loss of Function	3.98	5	27.6	0.181	0.00000159	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000115	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000115	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.910
• hipred: Y
• hipred_score: 0.696
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpp6

Gene ontology

• Biological process: protein-containing complex assembly
• Cellular component: plasma membrane;membrane;extracellular exosome
• Molecular function: protein binding;PDZ domain binding