ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:NLRP12

Protein Summary

Gene summary

Gene name: NLRP12
ASpdb.0 ID: 91662
	Gene
Gene symbol	NLRP12
Gene ID	91662
Gene name	NLR family pyrin domain containing 12
Synonyms	CLR19.3\|FCAS2\|NALP12\|PAN6\|PYPAF7\|RNO\|RNO2
Cytomap	19q13.42
Type of gene	protein-coding
Description	NACHT, LRR and PYD domains-containing protein 12PYRIN-containing APAF1-like protein 7monarch 1nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12regulated by nitric oxide
Modification date	20240403
UniProtAcc	P59046

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	NLRP12	GO:0001818	negative regulation of cytokine production	16203735
Gene	NLRP12	GO:0005634	nucleus	12019269
Gene	NLRP12	GO:0005737	cytoplasm	12019269
Gene	NLRP12	GO:0009968	negative regulation of signal transduction	16203735
Gene	NLRP12	GO:0031953	negative regulation of protein autophosphorylation	16203735
Gene	NLRP12	GO:0032088	negative regulation of NF-kappaB transcription factor activity	18230725
Gene	NLRP12	GO:0032692	negative regulation of interleukin-1 production	16203735
Gene	NLRP12	GO:0032715	negative regulation of interleukin-6 production	16203735
Gene	NLRP12	GO:0043122	regulation of canonical NF-kappaB signal transduction	12019269
Gene	NLRP12	GO:0043124	negative regulation of canonical NF-kappaB signal transduction	16203735
Gene	NLRP12	GO:0043281	regulation of cysteine-type endopeptidase activity involved in apoptotic process	12019269
Gene	NLRP12	GO:0045345	positive regulation of MHC class I biosynthetic process	12759408
Gene	NLRP12	GO:0045751	negative regulation of Toll signaling pathway	16203735
Gene	NLRP12	GO:1901223	negative regulation of non-canonical NF-kappaB signal transduction	17237370
Gene	NLRP12	GO:1901224	positive regulation of non-canonical NF-kappaB signal transduction	12019269

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
P59046-1	P59046-1_4xhs_A.pdb	4XHS	X-ray	1.7	A	27	106

ASpdb's canonical and alternatively spliced isoform information.

accession_id	gene_name	canonical_id	alternative_id	canonical_length	alternative_length	canonical_start	canonical_end	type	originalSEQ	variationSEQ	alternative_start	alternative_end
P59046	NLRP12	P59046-1	P59046-2	1061	1005	976	1031	Deletion	none	none	975	975
P59046	NLRP12	P59046-1	P59046-3	1061	949	862	973	Deletion	none	none	861	861
P59046	NLRP12	P59046-1	P59046-4	1061	891	862	1031	Deletion	none	none	861	861
P59046	NLRP12	P59046-1	P59046-5	1061	287	1	717	Deletion	none	none	0	0
P59046	NLRP12	P59046-1	P59046-5	1061	287	718	748	Substitution	LSLYRNALGSRGVKLLCQGLRHPNCKLQNLR	MSQAWWHTSVSPATQEAKAGGLLQPRRQRLW	1	31
P59046	NLRP12	P59046-1	P59046-5	1061	287	921	977	Deletion	none	none	203	203
P59046	NLRP12	P59046-1	P59046-6	1061	1004	920	976	Deletion	none	none	919	919

Multiple sequence alignment of our canonical and alternatively spliced NLRP12

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of NLRP12

UniProt-id	ENSG	ENST	ENSP
P59046-1	ENSG00000142405.23	ENST00000324134.11	ENSP00000319377.6
P59046-6	ENSG00000142405.23	ENST00000391775.7	ENSP00000375655.3

UniProt-id	NM ID	NP ID
P59046-1	NM_144687.3	NP_653288.1
P59046-6	NM_001277129.1	NP_001264058.1

Amino acid sequences of our canonical and alternatively spliced NLRP12

accession_id	Protein sequence
P59046-1	MLRTAGRDGLCRLSTYLEELEAVELKKFKLYLGTATELGEGKIPWGSMEKAGPLEMAQLLITHFGPEEAWRLALSTFERINRKDLWERGQ REDLVRDTPPGGPSSLGNQSTCLLEVSLVTPRKDPQETYRDYVRRKFRLMEDRNARLGECVNLSHRYTRLLLVKEHSNPMQVQQQLLDTG RGHARTVGHQASPIKIETLFEPDEERPEPPRTVVMQGAAGIGKSMLAHKVMLDWADGKLFQGRFDYLFYINCREMNQSATECSMQDLIFS CWPEPSAPLQELIRVPERLLFIIDGFDELKPSFHDPQGPWCLCWEEKRPTELLLNSLIRKKLLPELSLLITTRPTALEKLHRLLEHPRHV EILGFSEAERKEYFYKYFHNAEQAGQVFNYVRDNEPLFTMCFVPLVCWVVCTCLQQQLEGGGLLRQTSRTTTAVYMLYLLSLMQPKPGAP RLQPPPNQRGLCSLAADGLWNQKILFEEQDLRKHGLDGEDVSAFLNMNIFQKDINCERYYSFIHLSFQEFFAAMYYILDEGEGGAGPDQD VTRLLTEYAFSERSFLALTSRFLFGLLNEETRSHLEKSLCWKVSPHIKMDLLQWIQSKAQSDGSTLQQGSLEFFSCLYEIQEEEFIQQAL SHFQVIVVSNIASKMEHMVSSFCLKRCRSAQVLHLYGATYSADGEDRARCSAGAHTLLVQLPERTVLLDAYSEHLAAALCTNPNLIELSL YRNALGSRGVKLLCQGLRHPNCKLQNLRLKRCRISSSACEDLSAALIANKNLTRMDLSGNGVGFPGMMLLCEGLRHPQCRLQMIQLRKCQ LESGACQEMASVLGTNPHLVELDLTGNALEDLGLRLLCQGLRHPVCRLRTLWLKICRLTAAACDELASTLSVNQSLRELDLSLNELGDLG VLLLCEGLRHPTCKLQTLRLGICRLGSAACEGLSVVLQANHNLRELDLSFNDLGDWGLWLLAEGLQHPACRLQKLWLDSCGLTAKACENL
P59046-2	MLRTAGRDGLCRLSTYLEELEAVELKKFKLYLGTATELGEGKIPWGSMEKAGPLEMAQLLITHFGPEEAWRLALSTFERINRKDLWERGQ REDLVRDTPPGGPSSLGNQSTCLLEVSLVTPRKDPQETYRDYVRRKFRLMEDRNARLGECVNLSHRYTRLLLVKEHSNPMQVQQQLLDTG RGHARTVGHQASPIKIETLFEPDEERPEPPRTVVMQGAAGIGKSMLAHKVMLDWADGKLFQGRFDYLFYINCREMNQSATECSMQDLIFS CWPEPSAPLQELIRVPERLLFIIDGFDELKPSFHDPQGPWCLCWEEKRPTELLLNSLIRKKLLPELSLLITTRPTALEKLHRLLEHPRHV EILGFSEAERKEYFYKYFHNAEQAGQVFNYVRDNEPLFTMCFVPLVCWVVCTCLQQQLEGGGLLRQTSRTTTAVYMLYLLSLMQPKPGAP RLQPPPNQRGLCSLAADGLWNQKILFEEQDLRKHGLDGEDVSAFLNMNIFQKDINCERYYSFIHLSFQEFFAAMYYILDEGEGGAGPDQD VTRLLTEYAFSERSFLALTSRFLFGLLNEETRSHLEKSLCWKVSPHIKMDLLQWIQSKAQSDGSTLQQGSLEFFSCLYEIQEEEFIQQAL SHFQVIVVSNIASKMEHMVSSFCLKRCRSAQVLHLYGATYSADGEDRARCSAGAHTLLVQLPERTVLLDAYSEHLAAALCTNPNLIELSL YRNALGSRGVKLLCQGLRHPNCKLQNLRLKRCRISSSACEDLSAALIANKNLTRMDLSGNGVGFPGMMLLCEGLRHPQCRLQMIQLRKCQ LESGACQEMASVLGTNPHLVELDLTGNALEDLGLRLLCQGLRHPVCRLRTLWLKICRLTAAACDELASTLSVNQSLRELDLSLNELGDLG VLLLCEGLRHPTCKLQTLRLGICRLGSAACEGLSVVLQANHNLRELDLSFNDLGDWGLWLLAEGLQHPACRLQKLLWLFGMDLNKMTHSR
P59046-3	MLRTAGRDGLCRLSTYLEELEAVELKKFKLYLGTATELGEGKIPWGSMEKAGPLEMAQLLITHFGPEEAWRLALSTFERINRKDLWERGQ REDLVRDTPPGGPSSLGNQSTCLLEVSLVTPRKDPQETYRDYVRRKFRLMEDRNARLGECVNLSHRYTRLLLVKEHSNPMQVQQQLLDTG RGHARTVGHQASPIKIETLFEPDEERPEPPRTVVMQGAAGIGKSMLAHKVMLDWADGKLFQGRFDYLFYINCREMNQSATECSMQDLIFS CWPEPSAPLQELIRVPERLLFIIDGFDELKPSFHDPQGPWCLCWEEKRPTELLLNSLIRKKLLPELSLLITTRPTALEKLHRLLEHPRHV EILGFSEAERKEYFYKYFHNAEQAGQVFNYVRDNEPLFTMCFVPLVCWVVCTCLQQQLEGGGLLRQTSRTTTAVYMLYLLSLMQPKPGAP RLQPPPNQRGLCSLAADGLWNQKILFEEQDLRKHGLDGEDVSAFLNMNIFQKDINCERYYSFIHLSFQEFFAAMYYILDEGEGGAGPDQD VTRLLTEYAFSERSFLALTSRFLFGLLNEETRSHLEKSLCWKVSPHIKMDLLQWIQSKAQSDGSTLQQGSLEFFSCLYEIQEEEFIQQAL SHFQVIVVSNIASKMEHMVSSFCLKRCRSAQVLHLYGATYSADGEDRARCSAGAHTLLVQLPERTVLLDAYSEHLAAALCTNPNLIELSL YRNALGSRGVKLLCQGLRHPNCKLQNLRLKRCRISSSACEDLSAALIANKNLTRMDLSGNGVGFPGMMLLCEGLRHPQCRLQMIQLRKCQ LESGACQEMASVLGTNPHLVELDLTGNALEDLGLRLLCQGLRHPVCRLRTLKLWLDSCGLTAKACENLYFTLGINQTLTDLYLTNNALGD
P59046-4	MLRTAGRDGLCRLSTYLEELEAVELKKFKLYLGTATELGEGKIPWGSMEKAGPLEMAQLLITHFGPEEAWRLALSTFERINRKDLWERGQ REDLVRDTPPGGPSSLGNQSTCLLEVSLVTPRKDPQETYRDYVRRKFRLMEDRNARLGECVNLSHRYTRLLLVKEHSNPMQVQQQLLDTG RGHARTVGHQASPIKIETLFEPDEERPEPPRTVVMQGAAGIGKSMLAHKVMLDWADGKLFQGRFDYLFYINCREMNQSATECSMQDLIFS CWPEPSAPLQELIRVPERLLFIIDGFDELKPSFHDPQGPWCLCWEEKRPTELLLNSLIRKKLLPELSLLITTRPTALEKLHRLLEHPRHV EILGFSEAERKEYFYKYFHNAEQAGQVFNYVRDNEPLFTMCFVPLVCWVVCTCLQQQLEGGGLLRQTSRTTTAVYMLYLLSLMQPKPGAP RLQPPPNQRGLCSLAADGLWNQKILFEEQDLRKHGLDGEDVSAFLNMNIFQKDINCERYYSFIHLSFQEFFAAMYYILDEGEGGAGPDQD VTRLLTEYAFSERSFLALTSRFLFGLLNEETRSHLEKSLCWKVSPHIKMDLLQWIQSKAQSDGSTLQQGSLEFFSCLYEIQEEEFIQQAL SHFQVIVVSNIASKMEHMVSSFCLKRCRSAQVLHLYGATYSADGEDRARCSAGAHTLLVQLPERTVLLDAYSEHLAAALCTNPNLIELSL YRNALGSRGVKLLCQGLRHPNCKLQNLRLKRCRISSSACEDLSAALIANKNLTRMDLSGNGVGFPGMMLLCEGLRHPQCRLQMIQLRKCQ
P59046-5	MSQAWWHTSVSPATQEAKAGGLLQPRRQRLWLKRCRISSSACEDLSAALIANKNLTRMDLSGNGVGFPGMMLLCEGLRHPQCRLQMIQLR KCQLESGACQEMASVLGTNPHLVELDLTGNALEDLGLRLLCQGLRHPVCRLRTLWLKICRLTAAACDELASTLSVNQSLRELDLSLNELG DLGVLLLCEGLRHPTCKLQTLRLDSCGLTAKACENLYFTLGINQTLTDLYLTNNALGDTGVRLLCKRLSHPGCKLRVLWLFGMDLNKMTH
P59046-6	MLRTAGRDGLCRLSTYLEELEAVELKKFKLYLGTATELGEGKIPWGSMEKAGPLEMAQLLITHFGPEEAWRLALSTFERINRKDLWERGQ REDLVRDTPPGGPSSLGNQSTCLLEVSLVTPRKDPQETYRDYVRRKFRLMEDRNARLGECVNLSHRYTRLLLVKEHSNPMQVQQQLLDTG RGHARTVGHQASPIKIETLFEPDEERPEPPRTVVMQGAAGIGKSMLAHKVMLDWADGKLFQGRFDYLFYINCREMNQSATECSMQDLIFS CWPEPSAPLQELIRVPERLLFIIDGFDELKPSFHDPQGPWCLCWEEKRPTELLLNSLIRKKLLPELSLLITTRPTALEKLHRLLEHPRHV EILGFSEAERKEYFYKYFHNAEQAGQVFNYVRDNEPLFTMCFVPLVCWVVCTCLQQQLEGGGLLRQTSRTTTAVYMLYLLSLMQPKPGAP RLQPPPNQRGLCSLAADGLWNQKILFEEQDLRKHGLDGEDVSAFLNMNIFQKDINCERYYSFIHLSFQEFFAAMYYILDEGEGGAGPDQD VTRLLTEYAFSERSFLALTSRFLFGLLNEETRSHLEKSLCWKVSPHIKMDLLQWIQSKAQSDGSTLQQGSLEFFSCLYEIQEEEFIQQAL SHFQVIVVSNIASKMEHMVSSFCLKRCRSAQVLHLYGATYSADGEDRARCSAGAHTLLVQLPERTVLLDAYSEHLAAALCTNPNLIELSL YRNALGSRGVKLLCQGLRHPNCKLQNLRLKRCRISSSACEDLSAALIANKNLTRMDLSGNGVGFPGMMLLCEGLRHPQCRLQMIQLRKCQ LESGACQEMASVLGTNPHLVELDLTGNALEDLGLRLLCQGLRHPVCRLRTLWLKICRLTAAACDELASTLSVNQSLRELDLSLNELGDLG VLLLCEGLRHPTCKLQTLRLDSCGLTAKACENLYFTLGINQTLTDLYLTNNALGDTGVRLLCKRLSHPGCKLRVLWLFGMDLNKMTHSRL

Protein Functional Features

Main function of this protein. (from UniProt)

NLRP12 (go to UniProt):P59046

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
P59046	Domain	1	95	Note=Pyrin;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00061	Type=Deletion;Start=1;End=717
P59046	Domain	129	201	Note=FISNA;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1;End=717
P59046	Domain	211	528	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136	Type=Deletion;Start=1;End=717
P59046	Repeat	857	878	Note=LRR 2	Type=Deletion;Start=862;End=973
P59046	Repeat	857	878	Note=LRR 2	Type=Deletion;Start=862;End=1031
P59046	Repeat	885	906	Note=LRR 3	Type=Deletion;Start=862;End=973
P59046	Repeat	885	906	Note=LRR 3	Type=Deletion;Start=862;End=1031
P59046	Repeat	914	935	Note=LRR 4	Type=Deletion;Start=862;End=973
P59046	Repeat	914	935	Note=LRR 4	Type=Deletion;Start=862;End=1031
P59046	Repeat	914	935	Note=LRR 4	Type=Deletion;Start=921;End=977
P59046	Repeat	914	935	Note=LRR 4	Type=Deletion;Start=920;End=976
P59046	Repeat	942	962	Note=LRR 5	Type=Deletion;Start=862;End=973
P59046	Repeat	942	962	Note=LRR 5	Type=Deletion;Start=862;End=1031
P59046	Repeat	942	962	Note=LRR 5	Type=Deletion;Start=921;End=977
P59046	Repeat	942	962	Note=LRR 5	Type=Deletion;Start=920;End=976
P59046	Repeat	971	992	Note=LRR 6	Type=Deletion;Start=976;End=1031
P59046	Repeat	971	992	Note=LRR 6	Type=Deletion;Start=862;End=973
P59046	Repeat	971	992	Note=LRR 6	Type=Deletion;Start=862;End=1031
P59046	Repeat	971	992	Note=LRR 6	Type=Deletion;Start=921;End=977
P59046	Repeat	971	992	Note=LRR 6	Type=Deletion;Start=920;End=976
P59046	Repeat	999	1020	Note=LRR 7	Type=Deletion;Start=976;End=1031
P59046	Repeat	999	1020	Note=LRR 7	Type=Deletion;Start=862;End=1031
P59046	Repeat	1028	1049	Note=LRR 8	Type=Deletion;Start=976;End=1031
P59046	Repeat	1028	1049	Note=LRR 8	Type=Deletion;Start=862;End=1031

Gene Isoform Structures and Expression Levels for NLRP12

Gene structures of our canonical and alternative spliced genes of NLRP12
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of P59046-1

3D view using mol* of P59046-2

3D view using mol* of P59046-3

3D view using mol* of P59046-4

3D view using mol* of P59046-5

3D view using mol* of P59046-6

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of P59046-1

pLDDT distribution across the protein length of P59046-2

pLDDT distribution across the protein length of P59046-3

pLDDT distribution across the protein length of P59046-4

pLDDT distribution across the protein length of P59046-5

pLDDT distribution across the protein length of P59046-6

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of P59046-1

Ramachandran plot of P59046-2

Ramachandran plot of P59046-6

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
P59046-1	1.083	148	1.075	403.368	0.5	0.822	1.062	0.843	1.099	0.767	1.237	169,170,172,173,174,175,176,177,178,179,218,219,34 3,344,345,396,399,400,402,403,406,431,435,469,472, 474,514,515,516,518,519,551,553,554,555,557,558,56 1,645
P59046-2	1.082	327	1.019	755.972	0.422	0.82	1.093	0.479	1.268	0.378	1.29	163,165,167,170,171,172,173,174,175,176,177,178,17 9,180,181,182,185,186,187,188,189,190,191,218,219, 361,363,394,395,396,399,400,402,403,406,430,431,46 8,469,472,473,474,514,515,516,518,519,552,553,554, 555,557,558,561,611,612,615,618,619,639,640,642,64 3,645,646,649,668,669
P59046-3	1.038	408	1.054	1132.243	0.571	0.753	0.928	0.641	1.038	0.618	0.691	161,166,167,169,171,172,173,174,175,176,177,178,17 9,180,181,182,183,184,185,186,187,189,218,219,343, 344,345,346,347,348,349,363,365,366,367,370,392,39 3,394,395,396,398,399,400,402,430,431,468,469,472, 473,474,475,496,511,512,514,515,516,518,519,548,55 1,552,553,554,555,557,558,561,609,611,612,615,619, 642,643,644,645,646,649,669,670,695,697,753
P59046-4	1.089	185	0.977	445.9	0.449	0.831	1.044	0.396	1.415	0.28	0.984	161,163,164,165,166,167,171,172,175,176,183,184,18 6,187,188,189,190,191,192,217,218,221,344,347,361, 362,363,365,366,370,399,402,496,497,498,499,500,51 1,512,513,514
P59046-5	0.925	89	0.908	190.365	0.529	0.648	0.921	0.466	1.127	0.413	0.412	7,8,9,10,11,25,26,27,28,29,30,31,32,54,56,57
P59046-6	1.075	245	1.028	606.424	0.472	0.81	1.051	1.004	1.22	0.823	0.454	136,137,139,140,141,142,143,153,156,157,158,160,21 9,220,221,222,223,224,225,228,249,251,253,294,295, 297,298,343,365,373,377,404,405,408,495,498,500,50 1,502,513

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of P59046-1_P59046-1_4xhs_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P59046-1_4xhs_A_P59046-2.pdb

3D view using mol* of P59046-1_4xhs_A_P59046-3.pdb

3D view using mol* of P59046-1_4xhs_A_P59046-4.pdb

3D view using mol* of P59046-1_4xhs_A_P59046-5.pdb

3D view using mol* of P59046-1_4xhs_A_P59046-6.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P59046-1_P59046-2.pdb

3D view using mol* of P59046-1_P59046-3.pdb

3D view using mol* of P59046-1_P59046-4.pdb

3D view using mol* of P59046-1_P59046-5.pdb

3D view using mol* of P59046-1_P59046-6.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/P59046-1_vs_P59046-2.png