PALD1

phosphatase domain containing paladin 1

Basic information

Region (hg38): 10:70478767-70668754

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 (50 variants)
Aplastic anemia (24 variants)
Familial hemophagocytic lymphohistiocytosis (11 variants)
not provided (7 variants)
Inborn genetic diseases (5 variants)
Lymphoma, non-Hodgkin, familial;Aplastic anemia;Familial hemophagocytic lymphohistiocytosis 2 (4 variants)
Autoinflammatory syndrome (3 variants)
PRF1-related disorder (3 variants)
Familial hemophagocytic lymphohistiocytosis 2;Aplastic anemia;Lymphoma, non-Hodgkin, familial (2 variants)
Lymphoma, non-Hodgkin, familial;Familial hemophagocytic lymphohistiocytosis 2;Aplastic anemia (2 variants)
Aplastic anemia;Familial hemophagocytic lymphohistiocytosis 2;Lymphoma, non-Hodgkin, familial (1 variants)
Familial hemophagocytic lymphohistiocytosis 2;Lymphoma, non-Hodgkin, familial;Aplastic anemia (1 variants)
Familial hemophagocytic lymphohistiocytosis type 1 (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. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous	1 clinvar	1 clinvar		21 clinvar	2 clinvar	25
missense	4 clinvar	4 clinvar	98 clinvar	13 clinvar		119
nonsense				1 clinvar		1
start loss						0
frameshift	1 clinvar	2 clinvar				3
splice donor/acceptor (+/-2bp)						0
Total	6	7	98	35	2

Highest pathogenic variant AF is 0.000879831

Loading clinvar variants...

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

loftool
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_indispensability_pred
gene_indispensability_score

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
Phenotype

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