PIDD1 p53-induced death domain protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PIDD1provided by HGNC
Official Full Name: p53-induced death domain protein 1provided by HGNC
Primary source: HGNC:HGNC:16491
See related: Ensembl:ENSG00000177595 MIM:605247; AllianceGenome:HGNC:16491
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LRDD; PIDD; MRT75
Summary: The protein encoded by this gene contains a leucine-rich repeat and a death domain. This protein has been shown to interact with other death domain proteins, such as Fas (TNFRSF6)-associated via death domain (FADD) and MAP-kinase activating death domain-containing protein (MADD), and thus may function as an adaptor protein in cell death-related signaling processes. The expression of the mouse counterpart of this gene has been found to be positively regulated by the tumor suppressor p53 and to induce cell apoptosis in response to DNA damage, which suggests a role for this gene as an effector of p53-dependent apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]
Expression: Ubiquitous expression in testis (RPKM 3.7), spleen (RPKM 3.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.5

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (799184..809501, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (850616..861222, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (799184..805231, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Extra centrosomes induce PIDD1-mediated inflammation and immunosurveillance.
Title: Extra centrosomes induce PIDD1-mediated inflammation and immunosurveillance.
Molecular basis of neurodevelopmental disorders caused by pathogenic variants of PIDD.
Title: Molecular basis of neurodevelopmental disorders caused by pathogenic variants of PIDD.
Pathogenic variants in PIDD1 lead to an autosomal recessive neurodevelopmental disorder with pachygyria and psychiatric features.
Title: Pathogenic variants in PIDD1 lead to an autosomal recessive neurodevelopmental disorder with pachygyria and psychiatric features.
ATR signalling mediates the prosurvival function of phospho-NPM against PIDDosome mediated cell death.
Title: ATR signalling mediates the prosurvival function of phospho-NPM against PIDDosome mediated cell death.
Biallelic mutations in the death domain of PIDD1 impair caspase-2 activation and are associated with intellectual disability.
Title: Biallelic mutations in the death domain of PIDD1 impair caspase-2 activation and are associated with intellectual disability.
PIDD interaction with KEAP1 as a new mutation-independent mechanism to promote NRF2 stabilization and chemoresistance in NSCLC.
Title: PIDD interaction with KEAP1 as a new mutation-independent mechanism to promote NRF2 stabilization and chemoresistance in NSCLC.
Attention-deficit/hyperactivity disorder risk alleles correlated with increased expression (and decreased methylation) of ARTN and PIDD1 and with a decreased expression (and increased methylation) of C2orf82.
Title: Exploring genetic variation that influences brain methylation in attention-deficit/hyperactivity disorder.
Whole exome sequencing (WES) of an affected fetus, and subsequent Sanger sequencing of the second fetus, revealed a homozygous frameshift variant in CRADD, which encodes an adaptor protein that interacts with PIDD and caspase-2 to initiate apoptosis
Title: Homozygous null variant in CRADD, encoding an adaptor protein that mediates apoptosis, is associated with lissencephaly.
NPM1-dependent nucleolar PIDDosome is a key initiator of the caspase-2 activation cascade.
Title: NPM1 directs PIDDosome-dependent caspase-2 activation in the nucleolus.
PIDD expression was lower in HCC tissues and HCC cell lines, compared with the adjacent non-tumorous tissues and LO2 normal hepatocytes. PIDD could serve as an independent prognostic factor to predict the survival of HCC patients. PIDD facilitated cell cycle progression and accelerated cell proliferation in HepG2 cells, while overexpression of PIDD resulted in cell cycle arrest at G1 phase in Hep3B cells.
Title: Low expression of PIDD is associated with cell proliferation and apoptosis in hepatocellular carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly MedGen: C5676961 OMIM: 619827 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH123677 (e-PCR)
- UniSTS:138687

SGC30389 (e-PCR)
- UniSTS:82645

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables death receptor binding	TAS Traceable Author Statement more info	PubMed
enables endopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA damage response	NAS Non-traceable Author Statement more info	PubMed
involved_in DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in activation of cysteine-type endopeptidase activity involved in apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in extrinsic apoptotic signaling pathway via death domain receptors	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of NF-kappaB transcription factor activity	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of apoptotic process	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of apoptotic process	TAS Traceable Author Statement more info	PubMed
involved_in protein autoprocessing	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
part_of endopeptidase complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleolus	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: p53-induced death domain-containing protein 1

Names: leucine-rich repeat and death domain-containing protein; leucine-rich repeats and death domain containing; p53-induced protein with a death domain

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_145886.4 → NP_665893.2 p53-induced death domain-containing protein 1 isoform 1

See identical proteins and their annotated locations for NP_665893.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AF274972, BQ214414, BX349115, CN427946

Consensus CDS

CCDS7716.1

UniProtKB/Swiss-Prot

Q59FD1, Q59H10, Q59HC7, Q7Z4P8, Q8NC89, Q8NDL2, Q96C25, Q9HB75, Q9NRE6

Related

ENSP00000337797.5, ENST00000347755.10

Conserved Domains (6) summary

cd00116
Location:117 → 279

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd08779
Location:788 → 873

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:127 → 152

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:421 → 453

Peptidase_S68; Peptidase S68

pfam13855
Location:194 → 252

LRR_8; Leucine rich repeat

cl02517
Location:325 → 398

ZU5; ZU5 domain
NM_145887.4 → NP_665894.2 p53-induced death domain-containing protein 1 isoform 3

See identical proteins and their annotated locations for NP_665894.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.

Source sequence(s)

BC014904, BQ059356, BX349115, CN427946

Consensus CDS

CCDS44508.1

UniProtKB/Swiss-Prot

Q9HB75

Related

ENSP00000416801.2, ENST00000411829.6

Conserved Domains (7) summary

cd00116
Location:117 → 279

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd08779
Location:771 → 856

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:127 → 152

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:421 → 453

Peptidase_S68; Peptidase S68

pfam13855
Location:194 → 252

LRR_8; Leucine rich repeat

cl00467
Location:666 → 856

Ntn_hydrolase; The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a ...

cl02517
Location:325 → 398

ZU5; ZU5 domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

799184..809501 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011520210.4 → XP_011518512.1 p53-induced death domain-containing protein 1 isoform X4

See identical proteins and their annotated locations for XP_011518512.1

UniProtKB/Swiss-Prot

Q59FD1, Q59H10, Q59HC7, Q7Z4P8, Q8NC89, Q8NDL2, Q96C25, Q9HB75, Q9NRE6

Conserved Domains (6) summary

cd00116
Location:117 → 279

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd08779
Location:788 → 873

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:127 → 152

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:421 → 453

Peptidase_S68; Peptidase S68

pfam13855
Location:194 → 252

LRR_8; Leucine rich repeat

cl02517
Location:325 → 398

ZU5; ZU5 domain
XM_005253005.6 → XP_005253062.1 p53-induced death domain-containing protein 1 isoform X2

See identical proteins and their annotated locations for XP_005253062.1

Conserved Domains (6) summary

cd00116
Location:117 → 279

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd08779
Location:812 → 897

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:127 → 152

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:421 → 453

Peptidase_S68; Peptidase S68

pfam13855
Location:194 → 252

LRR_8; Leucine rich repeat

cl02517
Location:325 → 398

ZU5; ZU5 domain
XM_011520209.4 → XP_011518511.1 p53-induced death domain-containing protein 1 isoform X3

Conserved Domains (7) summary

cd00116
Location:144 → 306

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd08779
Location:798 → 883

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:154 → 179

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:448 → 480

Peptidase_S68; Peptidase S68

pfam13855
Location:221 → 279

LRR_8; Leucine rich repeat

cl00467
Location:693 → 883

Ntn_hydrolase; The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a ...

cl02517
Location:352 → 425

ZU5; ZU5 domain
XM_047427240.1 → XP_047283196.1 p53-induced death domain-containing protein 1 isoform X1
XM_047427239.1 → XP_047283195.1 p53-induced death domain-containing protein 1 isoform X12
XM_047427238.1 → XP_047283194.1 p53-induced death domain-containing protein 1 isoform X11
XM_005253006.6 → XP_005253063.1 p53-induced death domain-containing protein 1 isoform X2

See identical proteins and their annotated locations for XP_005253063.1

Conserved Domains (6) summary

cd00116
Location:117 → 279

LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

cd08779
Location:812 → 897

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:127 → 152

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:421 → 453

Peptidase_S68; Peptidase S68

pfam13855
Location:194 → 252

LRR_8; Leucine rich repeat

cl02517
Location:325 → 398

ZU5; ZU5 domain
XM_047427243.1 → XP_047283199.1 p53-induced death domain-containing protein 1 isoform X8
XM_047427242.1 → XP_047283198.1 p53-induced death domain-containing protein 1 isoform X7
XM_047427241.1 → XP_047283197.1 p53-induced death domain-containing protein 1 isoform X6
XM_011520212.3 → XP_011518514.1 p53-induced death domain-containing protein 1 isoform X5

See identical proteins and their annotated locations for XP_011518514.1

Conserved Domains (6) summary

cd08779
Location:666 → 751

Death_PIDD; Death Domain of p53-induced protein with a death domain

sd00033
Location:7 → 26

LRR_RI; leucine-rich repeat [structural motif]

pfam10461
Location:275 → 307

Peptidase_S68; Peptidase S68

pfam12799
Location:95 → 134

LRR_4; Leucine Rich repeats (2 copies)

pfam13855
Location:48 → 106

LRR_8; Leucine rich repeat

cl02517
Location:179 → 252

ZU5; ZU5 domain
XM_047427246.1 → XP_047283202.1 p53-induced death domain-containing protein 1 isoform X10
XM_011520213.3 → XP_011518515.1 p53-induced death domain-containing protein 1 isoform X9

Conserved Domains (3) summary

cd08779
Location:499 → 584

Death_PIDD; Death Domain of p53-induced protein with a death domain

pfam10461
Location:108 → 140

Peptidase_S68; Peptidase S68

cl02517
Location:12 → 85

ZU5; ZU5 domain
XM_047427245.1 → XP_047283201.1 p53-induced death domain-containing protein 1 isoform X9
XM_047427244.1 → XP_047283200.1 p53-induced death domain-containing protein 1 isoform X13

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

850616..861222 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054369310.1 → XP_054225285.1 p53-induced death domain-containing protein 1 isoform X2
XM_054369312.1 → XP_054225287.1 p53-induced death domain-containing protein 1 isoform X4
XM_054369309.1 → XP_054225284.1 p53-induced death domain-containing protein 1 isoform X1
XM_054369311.1 → XP_054225286.1 p53-induced death domain-containing protein 1 isoform X3
XM_054369314.1 → XP_054225289.1 p53-induced death domain-containing protein 1 isoform X2
XM_054369308.1 → XP_054225283.1 p53-induced death domain-containing protein 1 isoform X14
XM_054369318.1 → XP_054225293.1 p53-induced death domain-containing protein 1 isoform X8
XM_054369317.1 → XP_054225292.1 p53-induced death domain-containing protein 1 isoform X7
XM_054369316.1 → XP_054225291.1 p53-induced death domain-containing protein 1 isoform X6
XM_054369315.1 → XP_054225290.1 p53-induced death domain-containing protein 1 isoform X5
XM_054369322.1 → XP_054225297.1 p53-induced death domain-containing protein 1 isoform X10
XM_054369321.1 → XP_054225296.1 p53-induced death domain-containing protein 1 isoform X9
XM_054369320.1 → XP_054225295.1 p53-induced death domain-containing protein 1 isoform X9
XM_054369313.1 → XP_054225288.1 p53-induced death domain-containing protein 1 isoform X15
XM_054369319.1 → XP_054225294.1 p53-induced death domain-containing protein 1 isoform X16

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_018494.3: Suppressed sequence

Description

NM_018494.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.