PRDM15

Summary

PRDM15 (PR/SET domain 15, HGNC:13999) is a protein-coding gene on chromosome 21q22.3, encoding PR domain zinc finger protein 15 (P57071). Sequence-specific DNA-binding transcriptional regulator.

Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and promoter-specific chromatin binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II; regulation of signal transduction; and regulation of stem cell division. Located in nuclear body.

Source: NCBI Gene 63977 — RefSeq curated summary.

At a glance

• Gene–disease (curated): multiple congenital anomalies/dysmorphic syndrome (Moderate, GenCC)
• GWAS associations: 8
• Clinical variants (ClinVar): 256 total — 1 likely-pathogenic
• MANE Select transcript: NM_001040424

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13999
Approved symbol	PRDM15
Name	PR/SET domain 15
Location	21q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000141956
Ensembl biotype	protein_coding
OMIM	617692
Entrez	63977

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 6 retained_intron, 5 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000269844, ENST00000398548, ENST00000422911, ENST00000441787, ENST00000447016, ENST00000449395, ENST00000465955, ENST00000470586, ENST00000477633, ENST00000486812, ENST00000489661, ENST00000491486, ENST00000495217, ENST00000496124, ENST00000927550

RefSeq mRNA: 3 — MANE Select: NM_001040424 NM_001040424, NM_001282934, NM_022115

CCDS: CCDS13676, CCDS42932, CCDS63370

Canonical transcript exons

ENST00000398548 — 24 exons

Exon	Start	End
ENSE00000951413	41854566	41854818
ENSE00000951414	41847090	41847191
ENSE00000951415	41839623	41839853
ENSE00000951416	41837934	41838063
ENSE00001320360	41857176	41857329
ENSE00001327189	41859592	41859685
ENSE00003461883	41823318	41823449
ENSE00003504505	41836468	41836649
ENSE00003509158	41836113	41836207
ENSE00003511333	41815705	41815836
ENSE00003542838	41819582	41819701
ENSE00003561259	41802712	41802921
ENSE00003564993	41820095	41820174
ENSE00003565640	41825960	41826054
ENSE00003573987	41798225	41801722
ENSE00003580708	41810753	41810836
ENSE00003585719	41821903	41822037
ENSE00003594386	41860327	41860372
ENSE00003594566	41810154	41810329
ENSE00003638827	41821067	41821230
ENSE00003650421	41879270	41879344
ENSE00003667541	41804534	41804614
ENSE00003676963	41828166	41828333
ENSE00003686098	41835437	41835524

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 90.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.3740 / max 66.2645, expressed in 1527 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
190569	4.2701	1526
190566	0.0613	14
190568	0.0262	6
190567	0.0163	4

Top tissues by expression

246 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	90.24	gold quality
ileal mucosa	UBERON:0000331	83.40	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.44	gold quality
granulocyte	CL:0000094	80.94	gold quality
bone marrow cell	CL:0002092	80.78	gold quality
lymph node	UBERON:0000029	80.33	gold quality
oviduct epithelium	UBERON:0004804	79.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.07	gold quality
tonsil	UBERON:0002372	78.93	gold quality
tendon of biceps brachii	UBERON:0008188	78.65	silver quality
tibialis anterior	UBERON:0001385	78.57	silver quality
gastrocnemius	UBERON:0001388	77.82	gold quality
thymus	UBERON:0002370	77.53	silver quality
stromal cell of endometrium	CL:0002255	77.51	gold quality
muscle of leg	UBERON:0001383	77.48	gold quality
lower esophagus mucosa	UBERON:0035834	77.47	gold quality
vermiform appendix	UBERON:0001154	77.30	gold quality
apex of heart	UBERON:0002098	77.17	gold quality
bronchial epithelial cell	CL:0002328	77.00	gold quality
pancreatic ductal cell	CL:0002079	76.74	silver quality
tibia	UBERON:0000979	76.44	gold quality
bronchus	UBERON:0002185	76.41	gold quality
cortical plate	UBERON:0005343	76.38	gold quality
mucosa of stomach	UBERON:0001199	76.15	gold quality
middle temporal gyrus	UBERON:0002771	75.99	silver quality
skeletal muscle organ	UBERON:0014892	75.89	gold quality
colonic epithelium	UBERON:0000397	75.88	gold quality
spleen	UBERON:0002106	75.75	gold quality
visceral pleura	UBERON:0002401	75.68	gold quality
ganglionic eminence	UBERON:0004023	75.38	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.74
E-CURD-112	no	3.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting PRDM15, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-106A-3P	99.53	67.58	995
HSA-MIR-5088-3P	98.29	66.63	1310
HSA-MIR-338-3P	98.14	67.38	1137
HSA-MIR-514A-5P	96.94	65.49	801
HSA-MIR-5586-5P	96.29	68.02	685
HSA-MIR-2276-5P	96.27	65.85	937

Literature-anchored findings (GeneRIF, showing 6)

• Findings indicate that PR domain containing 15 protein (PRDM15) is important in both mouse and human induced pluripotent stem cells (iPSCs) reprogramming. (PMID:28740264)
• PRDM15 loss of function links NOTCH and WNT/PCP signaling to patterning defects in holoprosencephaly. (PMID:31950080)
• PRDM15 Is Associated with Risk of Chronic Obstructive Pulmonary Disease in a Rural Population in Chile. (PMID:32222710)
• Mutations in PRDM15 Are a Novel Cause of Galloway-Mowat Syndrome. (PMID:33593823)
• Proof-of-Concept Method to Study Uncharacterized Methyltransferases Using PRDM15. (PMID:36674842)
• The RNA methyltransferase METTL16 enhances cholangiocarcinoma growth through PRDM15-mediated FGFR4 expression. (PMID:37817227)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	PRDM15	ENSDARG00000098867
mus_musculus	Prdm15	ENSMUSG00000014039
rattus_norvegicus	Prdm15	ENSRNOG00000001620

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

PR domain zinc finger protein 15 — P57071 (reviewed: P57071)

Alternative names: PR domain-containing protein 15, Zinc finger protein 298

All UniProt accessions (4): A0A6Q8PFK1, E7ER26, P57071, Q4W8S1

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific DNA-binding transcriptional regulator. Plays a role as a molecular node in a transcriptional network regulating embryonic development and cell fate decision. Stimulates the expression of upstream key transcriptional activators and repressors of the Wnt/beta-catenin and MAPK/ERK pathways, respectively, that are essential for naive pluripotency and self-renewal maintenance of embryonic stem cells (ESCs). Specifically promotes SPRY1 and RSPO1 transcription activation through recognition and direct binding of a specific DNA sequence in their promoter regions. Involved in early embryo development. Also plays a role in induced pluripotent stem cells (iPSCs) reprogramming.

Subunit / interactions. Interacts with Zincore complex components QRICH1 and SEPHS1; probably stabilizing PRDM15 at DNA-binding sites across the genome.

Subcellular location. Nucleus.

Tissue specificity. Detected in all tissues examined.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the class V-like SAM-binding methyltransferase superfamily.

Isoforms (5)

UniProt ID	Names	Canonical?
P57071-7	6, ZNF298a	yes
P57071-1	1
P57071-2	2, ZNF298b
P57071-5	4, ZNF298c
P57071-6	5, ZNF298d

RefSeq proteins (3): NP_001035514, NP_001269863, NP_071398 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001214	SET_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR044409	PRDM15_PR-SET	Domain
IPR046341	SET_dom_sf	Homologous_superfamily
IPR059126	Znf-C2H2_PRDM15	Domain

Pfam: PF00096, PF13894, PF21549, PF23573

UniProt features (39 total): zinc finger region 16, splice variant 8, compositionally biased region 5, region of interest 4, sequence conflict 2, chain 1, domain 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P57071-F1	56.66	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 517

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_STEM_CELL_DIVISION, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_REGULATION_OF_CELL_DIVISION, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, GOBP_POSITIVE_REGULATION_OF_CANONICAL_WNT_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY, chr21q22, GOBP_METHYLATION, GOMF_CHROMATIN_BINDING, GOCC_NUCLEAR_BODY, GOBP_CELL_DIVISION, JEPSEN_SMRT_TARGETS

GO Biological Process (6): regulation of transcription by RNA polymerase II (GO:0006357), methylation (GO:0032259), negative regulation of MAPK cascade (GO:0043409), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of canonical Wnt signaling pathway (GO:0090263), regulation of stem cell division (GO:2000035)

GO Molecular Function (9): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), methyltransferase activity (GO:0008168), zinc ion binding (GO:0008270), promoter-specific chromatin binding (GO:1990841), DNA binding (GO:0003677), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
metabolic process	1
MAPK cascade	1
regulation of MAPK cascade	1
negative regulation of intracellular signal transduction	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
positive regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
stem cell division	1
regulation of cell division	1
cis-regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transferase activity, transferring one-carbon groups	1
transition metal ion binding	1
chromatin binding	1
nucleic acid binding	1
binding	1
catalytic activity	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1248 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRDM15	SETD4	Q9NVD3	616
PRDM15	PRDM8	Q9NQV8	517
PRDM15	SMYD5	Q6GMV2	490
PRDM15	C2CD2	Q9Y426	488
PRDM15	CDCP2	Q5VXM1	486
PRDM15	SMIM15	Q7Z3B0	472
PRDM15	SMYD4	Q8IYR2	450
PRDM15	MCTP2	Q6DN12	431
PRDM15	UNC80	Q8N2C7	426
PRDM15	CMC2	Q9NRP2	423
PRDM15	TP53I11	O14683	423
PRDM15	MAST4	O15021	423
PRDM15	COL19A1	Q14993	417
PRDM15	SMYD3	Q9H7B4	414
PRDM15	TP53	P04637	412

IntAct

86 interactions, top by confidence:

A	B	Type	Score
H1-1	RRP8	psi-mi:“MI:0914”(association)	0.640
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
PRR11	NVL	psi-mi:“MI:0914”(association)	0.530
RPL30	RRP8	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZC3HAV1	KHNYN	psi-mi:“MI:0914”(association)	0.530
H1-4	RRP8	psi-mi:“MI:0914”(association)	0.530
RPL8	ZBTB24	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
H1-1	SURF6	psi-mi:“MI:0914”(association)	0.530
PRDM15	H1-5	psi-mi:“MI:0915”(physical association)	0.400
PRDM15	PRKCSH	psi-mi:“MI:0915”(physical association)	0.400
NFATC1	SMARCA5	psi-mi:“MI:0914”(association)	0.350
ZC3HAV1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.350
ZNF490	NEMF	psi-mi:“MI:0914”(association)	0.350
rl3_rl3l_human	NKRF	psi-mi:“MI:0914”(association)	0.350
RPL31	RPSA2	psi-mi:“MI:0914”(association)	0.350
SRP14	RPSA2	psi-mi:“MI:0914”(association)	0.350
RPS19	ZNF320	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL28	GTPBP10	psi-mi:“MI:0914”(association)	0.350
ILF3	GTPBP10	psi-mi:“MI:0914”(association)	0.350
RPL13A	GTPBP10	psi-mi:“MI:0914”(association)	0.350
ABT1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
OASL	ZNF316	psi-mi:“MI:0914”(association)	0.350

BioGRID (96): PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Proximity Label-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-MS), PRDM15 (Affinity Capture-RNA), PRDM15 (Affinity Capture-MS), PRDM15 (Proximity Label-MS), PRDM15 (Proximity Label-MS)

ESM2 similar proteins: A0JPB4, A1L1J6, A1L1R6, A1Z9R4, A2A935, A4IFJ6, E9Q6W4, E9Q8T2, G5E8B9, O08961, O13089, O15060, O42410, O57415, O73590, O95625, P14404, P57071, Q03112, Q03267, Q09452, Q13422, Q1L8W0, Q2M1K9, Q5DU09, Q5R9W9, Q5T0B9, Q5ZLR2, Q60821, Q62947, Q64318, Q6DBW0, Q6GNP2, Q6INV8, Q6KAS7, Q6NRM0, Q6NUD7, Q7TS63, Q802Y8, Q80TS5

Diamond homologs: A0A163UT06, A2AGX3, A6QPM3, B8A5Y1, E9Q3T6, E9Q8T2, O75626, P0C6Y7, P14404, P57071, Q3UZD5, Q5R5M1, Q60636, Q6P2A1, Q80V63, Q96EQ9, Q9GZV8, Q9NQV5, Q9NQV7, Q9NQW5, Q9NQX0, Q9QZP2, Q9UKN5, A2BID7, B4F6U4, Q3UTQ7, Q5RAX9, Q9NQV6, Q93560, Q9H4Q3, A1L2U9, B1WAZ8, B1WBU4, Q02026, Q0IH98, Q0VCJ6, Q65XX7, Q6P882, Q8K3J5, Q96BR9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 93 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of Senescence-Associated Heterochromatin Foci (SAHF)	5	58.9×	1e-07
Peptide chain elongation	20	44.5×	8e-27
Viral mRNA Translation	20	44.5×	8e-27
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	20	44.0×	8e-27
Selenocysteine synthesis	20	42.2×	1e-26
Eukaryotic Translation Termination	20	42.2×	1e-26
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	20	41.3×	1e-26
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	20	41.3×	1e-26

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of DNA recombination	6	75.7×	1e-08
chromosome condensation	6	56.8×	6e-08
cytoplasmic translation	21	43.7×	7e-27
translation	18	20.8×	7e-17
ribosomal small subunit biogenesis	7	17.9×	8e-06
regulation of alternative mRNA splicing, via spliceosome	5	13.7×	1e-03
rRNA processing	8	12.7×	1e-05
nucleosome assembly	8	12.6×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

256 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	204
Likely benign	18
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
871179	NM_001040424.3(PRDM15):c.2420G>A (p.Cys807Tyr)	Likely pathogenic

SpliceAI

5830 predictions. Top by Δscore:

Variant	Effect	Δscore
21:41801719:CTAC:C	acceptor_gain	1.0000
21:41802708:TGA:T	donor_loss	1.0000
21:41802709:GACC:G	donor_loss	1.0000
21:41802710:ACCT:A	donor_loss	1.0000
21:41802711:CC:C	donor_loss	1.0000
21:41802711:CCTG:C	donor_gain	1.0000
21:41802918:CAGG:C	acceptor_gain	1.0000
21:41802919:AGG:A	acceptor_gain	1.0000
21:41802922:C:CC	acceptor_gain	1.0000
21:41804531:CA:C	donor_loss	1.0000
21:41804611:GCAC:G	acceptor_gain	1.0000
21:41804612:CAC:C	acceptor_gain	1.0000
21:41804612:CACC:C	acceptor_gain	1.0000
21:41804613:AC:A	acceptor_gain	1.0000
21:41804614:CC:C	acceptor_gain	1.0000
21:41804615:C:A	acceptor_loss	1.0000
21:41804615:C:CC	acceptor_gain	1.0000
21:41810326:CCCA:C	acceptor_gain	1.0000
21:41810327:CCAC:C	acceptor_gain	1.0000
21:41810328:CACTT:C	acceptor_gain	1.0000
21:41810330:C:CC	acceptor_gain	1.0000
21:41810332:T:TC	acceptor_gain	1.0000
21:41810335:C:CT	acceptor_gain	1.0000
21:41810337:C:CT	acceptor_gain	1.0000
21:41810339:C:CT	acceptor_gain	1.0000
21:41810341:C:CT	acceptor_gain	1.0000
21:41810349:C:CT	acceptor_gain	1.0000
21:41810351:CACA:C	acceptor_gain	1.0000
21:41810353:CA:C	acceptor_gain	1.0000
21:41810354:A:AC	acceptor_gain	1.0000

AlphaMissense

7891 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:41810175:G:C	H1243Q	1.000
21:41810175:G:T	H1243Q	1.000
21:41810176:T:C	H1243R	1.000
21:41810177:G:C	H1243D	1.000
21:41810177:G:T	H1243N	1.000
21:41810214:G:C	C1230W	1.000
21:41810215:C:G	C1230S	1.000
21:41810215:C:T	C1230Y	1.000
21:41810216:A:G	C1230R	1.000
21:41810216:A:T	C1230S	1.000
21:41810223:G:C	C1227W	1.000
21:41810224:C:G	C1227S	1.000
21:41810224:C:T	C1227Y	1.000
21:41810225:A:G	C1227R	1.000
21:41810225:A:T	C1227S	1.000
21:41810254:A:G	L1217P	1.000
21:41810262:G:C	H1214Q	1.000
21:41810262:G:T	H1214Q	1.000
21:41810264:G:C	H1214D	1.000
21:41810272:A:G	L1211P	1.000
21:41810301:G:C	C1201W	1.000
21:41810302:C:A	C1201F	1.000
21:41810302:C:G	C1201S	1.000
21:41810302:C:T	C1201Y	1.000
21:41810303:A:G	C1201R	1.000
21:41810303:A:T	C1201S	1.000
21:41810310:G:C	C1198W	1.000
21:41810311:C:T	C1198Y	1.000
21:41810312:A:G	C1198R	1.000
21:41810759:G:C	H1190D	1.000

dbSNP variants (sampled 300 via entrez): RS1000015896 (21:41829364 C>T), RS1000056256 (21:41825742 C>T), RS1000117345 (21:41860263 G>A,T), RS1000120653 (21:41841954 A>T), RS1000165857 (21:41856724 C>T), RS1000193105 (21:41816623 G>A), RS1000268871 (21:41850433 G>C), RS1000299848 (21:41850627 G>T), RS1000312516 (21:41845737 T>C), RS1000395759 (21:41861749 T>G), RS1000396681 (21:41811915 G>A,C,T), RS1000412750 (21:41816807 G>A), RS1000501081 (21:41858011 C>G,T), RS1000520307 (21:41813545 C>T), RS1000552037 (21:41857812 C>T)

Disease associations

OMIM: gene MIM:617692 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
multiple congenital anomalies/dysmorphic syndrome	Moderate	Autosomal recessive

Mondo (2): pervasive developmental disorder (MONDO:0000594), multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)

Orphanet (1): Rare pervasive developmental disorder (Orphanet:168778)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST000371_8	Tanning	3.000000e-06
GCST001430_1	Parkinson’s disease	5.000000e-06
GCST001694_12	Response to taxane treatment (paclitaxel)	7.000000e-06
GCST005945_2	ADAMTS13 levels	7.000000e-09
GCST009391_1483	Metabolite levels	8.000000e-06
GCST010249_1	Chronic obstructive pulmonary disease	2.000000e-07
GCST010727_45	Deep white matter hyperintensities	6.000000e-06
GCST011435_2	Chronic obstructive pulmonary disease	9.000000e-07

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004279	suntan
EFO:0008011	a disintegrin and metalloproteinase with thrombospondin motifs 13 measurement
EFO:0010414	triacylglycerol 52:2 measurement
EFO:0005665	white matter hyperintensity measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D002659	Child Development Disorders, Pervasive	F03.625.164

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects expression, decreases expression	3
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	2
Acrolein	affects cotreatment, increases expression, increases abundance	2
Ozone	affects cotreatment, increases expression, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
trichostatin A	affects expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Air Pollutants	increases abundance, increases expression, affects cotreatment	1
Arsenic	affects methylation	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Gallic Acid	decreases expression	1
Methapyrilene	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin B1	increases methylation	1
Asbestos, Crocidolite	decreases methylation	1
Antirheumatic Agents	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

31 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT00205699	PHASE4	COMPLETED	Metabolic Effects of Antipsychotics in Children
NCT01238575	PHASE4	COMPLETED	Guanfacine for the Treatment of Hyperactivity in Pervasive Developmental Disorder
NCT02199925	PHASE4	UNKNOWN	An Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT00399698	PHASE3	COMPLETED	Study to Determine Whether There Are Any Cognitive or Motor Effects From Taking the Medicine Risperidone.
NCT00870727	PHASE3	COMPLETED	Study of Aripiprazole in the Treatment of Pervasive Developmental Disorders
NCT02985749	PHASE3	COMPLETED	A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT00198055	PHASE2	COMPLETED	A Study of Aripiprazole in Children and Adolescents With Aspergers and Pervasive Developmental Disorder.
NCT00308074	PHASE2	COMPLETED	An Open-Label Trial of Aripiprazole in Autism Spectrum Disorders
NCT01602016	PHASE2	TERMINATED	A Folinic Acid Intervention for Autism Spectrum Disorders
NCT05664841	PHASE2	RECRUITING	The Impact of a Virtual Magic Trick Training Program
NCT00325572	PHASE1	TERMINATED	Evaluation and Treatment of Copper/Zinc Imbalance in Children With Autism
NCT00773812	PHASE1	COMPLETED	Placebo-Controlled Pilot Trial of Mecamylamine for Treatment of Autism Spectrum Disorders
NCT01243905	PHASE2/PHASE3	UNKNOWN	Group Psychoeducational Program for Mothers of Children With High Functional Pervasive Developmental Disorders
NCT00318162	PHASE1/PHASE2	UNKNOWN	Trial of Low-Dose Naltrexone for Children With Pervasive Developmental Disorder (PDD)
NCT00004458	Not specified	TERMINATED	Longitudinal and Biological Study of Childhood Disintegrative Disorder
NCT00025779	Not specified	COMPLETED	Methylphenidate in Children and Adolescents With Pervasive Developmental Disorders
NCT00464477	Not specified	COMPLETED	Advanced Grandparental Age as a Risk Factor for Autism
NCT00531830	Not specified	UNKNOWN	Assessment of Factors Which Predict Improvement in Children With PDD After a Year of Integrative Therapy
NCT00579267	Not specified	COMPLETED	Reliability and Validity of the MINI International Neuropsychiatric Interview for Children and Adolescents (MINI-KID)
NCT00902798	Not specified	COMPLETED	Cognitive Enhancement Therapy for Adult Autism Spectrum Disorder
NCT01160783	Not specified	ACTIVE_NOT_RECRUITING	Genetic Contributions to Autism Spectrum Disorders
NCT01553240	Not specified	TERMINATED	Neurocircuitry of Autism- fMRI and Transcranial Magnetic Stimulation Studies
NCT01631851	Not specified	COMPLETED	Cognitive-Behavioral Therapy for Irritability in Adolescents With High Functioning Autism Spectrum Disorder
NCT01808066	Not specified	COMPLETED	GroundsKeeper: A Qualitative Study of Applied Game-based Interactives in Special Education Programs
NCT01921244	Not specified	COMPLETED	Shared Decision Making to Improve Care and Outcomes for Children With Autism
NCT03170453	Not specified	COMPLETED	Confirmatory Efficacy Trial of Cognitive Enhancement Therapy for Adult Autism Spectrum Disorder
NCT03177590	Not specified	COMPLETED	Recording Facial and Vocal Emotional Productions in Children With Autism as Part of the JEMImE Project
NCT03560453	Not specified	COMPLETED	Facilitating Employment for Youth With Autism
NCT03602378	Not specified	UNKNOWN	QoL and Stress in Parents of Children With Developmental Disabilities and Chronic Disease
NCT04654260	Not specified	ACTIVE_NOT_RECRUITING	Behavior Therapy for Irritability in Autism
NCT04788537	Not specified	COMPLETED	Services to Enhance Social Functioning in Adults With Autism Spectrum Disorders