PALD1

phosphatase domain containing paladin 1

Basic information

Region (hg38): 10:70478766-70668754

Previous symbols: [ "PALD", "KIAA1274" ]

Links

ENSG00000107719 ∙ NCBI:27143 ∙ OMIM:614656 ∙ HGNC:23530 ∙ Uniprot:Q9ULE6 ∙ 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 PALD1 gene.

• Familial hemophagocytic lymphohistiocytosis 2 (483 variants)
• not provided (73 variants)
• Inborn genetic diseases (71 variants)
• Aplastic anemia (70 variants)
• not specified (47 variants)
• Autoinflammatory syndrome (46 variants)
• Familial hemophagocytic lymphohistiocytosis (24 variants)
• Lymphoma, non-Hodgkin, familial (12 variants)
• PRF1-related condition (8 variants)
• Lymphoma, non-Hodgkin, familial;Familial hemophagocytic lymphohistiocytosis 2;Aplastic anemia (4 variants)
• Lymphoma, non-Hodgkin, familial;Aplastic anemia;Familial hemophagocytic lymphohistiocytosis 2 (4 variants)
• Aplastic anemia;Familial hemophagocytic lymphohistiocytosis 2;Lymphoma, non-Hodgkin, familial (2 variants)
• Familial hemophagocytic lymphohistiocytosis 2;Lymphoma, non-Hodgkin, familial;Aplastic anemia (2 variants)
• Aplastic anemia;Lymphoma, non-Hodgkin, familial;Familial hemophagocytic lymphohistiocytosis 2 (2 variants)
• See cases (2 variants)
• Hemophagocytic lymphohistiocytosis, familial, 2, susceptibility to (1 variants)
• Familial hemophagocytic lymphohistiocytosis 2;Aplastic anemia;Lymphoma, non-Hodgkin, familial (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALD1 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	1			15	2	18
missense	3	5	56	10		74
nonsense				1		1
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1	2	1	1	5
non coding	47	45	216	125	14	447
Total	53	50	272	151	16

Highest pathogenic variant AF is 0.000880

Variants in PALD1

This is a list of pathogenic ClinVar variants found in the PALD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-70525983-C-T		not specified	Uncertain significance (May 17, 2023)
10-70529223-C-A			Benign (Dec 31, 2019)
10-70529224-C-G			Likely benign (Feb 01, 2023)
10-70529272-A-G		not specified	Uncertain significance (Dec 19, 2022)
10-70529285-C-T		not specified	Uncertain significance (Aug 28, 2023)
10-70529294-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-70529300-C-T		not specified	Uncertain significance (Feb 05, 2024)
10-70529908-G-A		not specified	Uncertain significance (Feb 28, 2023)
10-70529931-G-A		not specified	Likely benign (Jul 12, 2022)
10-70530036-G-A		not specified	Uncertain significance (Nov 04, 2023)
10-70531344-G-A		not specified	Uncertain significance (Oct 27, 2022)
10-70531351-T-G		not specified	Uncertain significance (Nov 18, 2022)
10-70532644-C-G		not specified	Uncertain significance (Feb 01, 2023)
10-70532685-G-C		not specified	Uncertain significance (May 27, 2022)
10-70532693-C-A		not specified	Uncertain significance (Dec 08, 2023)
10-70532705-G-T		not specified	Uncertain significance (Dec 28, 2022)
10-70532706-C-T		not specified	Uncertain significance (Sep 22, 2023)
10-70532714-G-A		not specified	Uncertain significance (Jun 28, 2023)
10-70532735-A-T		not specified	Uncertain significance (Feb 10, 2022)
10-70533060-G-C		not specified	Uncertain significance (Jul 17, 2023)
10-70533928-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-70533946-C-T			Likely benign (Mar 29, 2018)
10-70533947-G-A		not specified	Uncertain significance (Dec 16, 2023)
10-70533997-G-A		not specified	Uncertain significance (Jan 02, 2024)
10-70534015-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALD1	protein_coding	protein_coding	ENST00000263563	19	89629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.06e-15	0.861	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.832	484	538	0.899	0.0000344	5541
Missense in Polyphen		111	128.6	0.86316		1289
Synonymous	0.479	220	229	0.960	0.0000153	1706
Loss of Function	2.06	30	44.9	0.668	0.00000235	469

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000713	0.000696
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000237	0.000231
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000110	0.000109
South Asian	0.000262	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.08

Haploinsufficiency Scores

• pHI: 0.593
• hipred: Y
• hipred_score: 0.600
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pald1

Zebrafish Information Network

• Gene name: pald1b
• Affected structure: central artery
• Phenotype tag: abnormal
• Phenotype quality: decreased branchiness

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation
• Cellular component: cytoplasm;cytosol
• Molecular function: protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;protein binding