PiSITE

PDB ID	3BXJ	CHAIN	A
Protein name	Ras GTPase-activating protein SynGAP
Uniprot Accession	Q9QUH6
The number of similar proteins	1
The number of binding states	1
The number of binding partners	0

Coloring

Unicolor (beige)

The number of binding partners

Group

Binding state	Binding partners
	3BXJ (CHAIN: A)
1	Monomeric state

Downdload

Molecule viewer

Only interaction residues

#binding
partners

Sequence information

PNKDNSRRVD

NVLKLWIIEA

RELPPKKRYY

CELCLDDMLY

ARTTSKPRSA

SGDTVFWGEH

FEFNNLPAVR

ALRLHLYRDS

DKKRKKDKAG

YVGLVTVPVA

100

101

TLAGRHFTEQ

WYPVTLPTGS

GGSGGMGSGG

GGGSGGGSGG

KGKGGCPAVR

150

151

LKARYQTMSI

LPMELYKEFA

EYVTNHYRML

CAVLEPALNV

KGKEEVASAL

200

201

VHILQSTGKA

KDFLSDMAMS

EVDRFMEREH

LIFRENTLAT

KAIEEYMRLI

250

251

GQKYLKDAIG

EFIRALYESE

ENCEVDPIKC

TASSLAEHQA

NLRMCCELAL

300

301

CKVVNSHCVF

PRELKEVFAS

WRLRCAERGR

EDIADRLISA

SLFLRFLCPA

350

351

IMSPSLFGLM

QEYPDEQTSR

TLTLIAKVIQ

NLANFSKFTS

KEDFLGFMNE

400

401

FLELEWGSMQ

QFLYEISNLD

TLTNSSSFEG

YIDLGRELST

LHALLWEVLP

450

451

QLSKEALLKL

GPLPRLLSDI

STALRNPNIQ

RQP

500

Variants

Residue	AA	Source	dbSNP	Clinical Significance	Allele Frequency (> 0.0001)	Disease name
241_ASN	SER	ClinVar chr6:33405449	-	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
295_GLU	ASP	ClinVar chr6:33405612	rs1760890843	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
295_GLU	GLY	ClinVar chr6:33405611	-	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
298_GLU	TER	ClinVar chr6:33405619	rs1554121207	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
347_TRP	ARG	ClinVar chr6:33405766	rs1581987445	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
348_TYR	TER	ClinVar chr6:33405771	-	Pathogenic	-	Inborn genetic diseases [MeSH:D030342,MedGen:C0950123]
387_LEU	ARG	ClinVar chr6:33405887	rs1554121265	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
400_GLU	TER	ClinVar chr6:33405925	rs1554121273	Pathogenic	-	not provided [MedGen:C3661900]
404_GLU	TER	ClinVar chr6:33405937	rs2151170014	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
405_PHE	SER	ClinVar chr6:33405941	rs1760905358	Likely pathogenic	-	Intellectual disability [Human Phenotype Ontology:HP:0000730,Human Phenotype Ontology:HP:0001249,Human Phenotype Ontology:HP:0001267,Human Phenotype Ontology:HP:0001286,Human Phenotype Ontology:HP:0002122,Human Phenotype Ontology:HP:0002192,Human Phenotype Ontology:HP:0002316,Human Phenotype Ontology:HP:0002382,Human Phenotype Ontology:HP:0002386,Human Phenotype Ontology:HP:0002402,Human Phenotype Ontology:HP:0002458,Human Phenotype Ontology:HP:0002482,Human Phenotype Ontology:HP:0002499,Human Phenotype Ontology:HP:0002543,Human Phenotype Ontology:HP:0003767,Human Phenotype Ontology:HP:0006833,Human Phenotype Ontology:HP:0007154,Human Phenotype Ontology:HP:0007176,Human Phenotype Ontology:HP:0007180,MONDO:MONDO:0001071,MeSH:D008607,MedGen:C3714756]
408_TYR	TER	ClinVar chr6:33405951	rs1561785045	Pathogenic	-	Inborn genetic diseases [MeSH:D030342,MedGen:C0950123]
408_TYR	TER	ClinVar chr6:33405951	rs1561785045	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
413_TYR	TER	ClinVar chr6:33405966	rs2151170078	Pathogenic	-	not provided\|Inborn genetic diseases [MedGen:C3661900\|MeSH:D030342,MedGen:C0950123]
416_LEU	PRO	ClinVar chr6:33405974	rs1581987885	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
418_ALA	VAL	gnomAD chr6:33405980	rs200213875	-	0.00033298	-
450_LEU	PRO	ClinVar chr6:33406203	rs2151170996	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
453_MET	LYS	ClinVar chr6:33406212	rs763770519	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
470_ARG	HIS	8.3kJPN chr6:33406263	rs1248933822	-	0.0001	-
479_ILE	ARG	ClinVar chr6:33406290	rs2151171287	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
491_LEU	PRO	ClinVar chr6:33406326	rs1760918521	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
495_ILE	SER	ClinVar chr6:33406338	rs1554121364	Likely pathogenic	-	not provided [MedGen:CN517202]
496_GLY	ARG	ClinVar chr6:33406340	rs1554121365	Pathogenic	-	not provided [MedGen:CN517202]
496_GLY	ARG	ClinVar chr6:33406340	-	Likely pathogenic	-	Inborn genetic diseases [MeSH:D030342,MedGen:C0950123]
497_GLU	TER	ClinVar chr6:33406554	rs2151172286	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
504_GLU	ALA	ClinVar chr6:33406576	rs1760931697	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
525_GLN	TER	ClinVar chr6:33406638	rs1554121438	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
529_ARG	TER	ClinVar chr6:33406650	rs1554121443	Pathogenic	-	Intellectual disability, autosomal dominant 5\|not provided\|Inborn genetic diseases [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621\|MedGen:C3661900\|MeSH:D030342,MedGen:C0950123]
532_CYS	TYR	ClinVar chr6:33406660	rs2151172652	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
536_LEU	PRO	ClinVar chr6:33406672	rs1554121453	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
554_PHE	SER	ClinVar chr6:33408535	-	Likely pathogenic	-	not provided [MedGen:CN517202]
556_SER	TER	ClinVar chr6:33408541	rs1554121682	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
557_TRP	TER	ClinVar chr6:33408545	rs1057518178	Pathogenic	-	not provided [MedGen:CN517202]
557_TRP	SER	ClinVar chr6:33408544	rs1554121684	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
558_ARG	LEU	ClinVar chr6:33408547	rs1554121685	Likely pathogenic	-	Inborn genetic diseases [MeSH:D030342,MedGen:C0950123]
558_ARG	GLN	ClinVar chr6:33408547	rs1554121685	Likely pathogenic	-	not provided [MedGen:C3661900]
561_CYS	TER	ClinVar chr6:33408557	-	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
564_ARG	TER	ClinVar chr6:33408564	rs121918316	Pathogenic	-	Intellectual disability, autosomal dominant 5\|not provided\|Inborn genetic diseases [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621\|MedGen:C3661900\|MeSH:D030342,MedGen:C0950123]
566_ARG	GLN	8.3kJPN chr6:33408571	-	-	0.0001	-
573_LEU	HIS	ClinVar chr6:33408592	rs1064795645	Likely pathogenic	-	not provided [MedGen:CN517202]
576_ALA	THR	8.3kJPN chr6:33408600	rs946029100	-	0.0001	-
606_ARG	TER	ClinVar chr6:33408690	rs1060503386	Pathogenic	-	Intellectual disability, autosomal dominant 5\|Complex neurodevelopmental disorder\|Neurodevelopmental delay\|not provided [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621\|MONDO:MONDO:0100038,MedGen:C5568766\|Human Phenotype Ontology:HP:0012758,MedGen:C4022738\|MedGen:C3661900]
615_ILE	VAL	gnomAD chr6:33408717	rs192497085	-	0.000202825	-
616_GLN	TER	ClinVar chr6:33408720	rs1554121729	Pathogenic	-	Inborn genetic diseases [MeSH:D030342,MedGen:C0950123]
618_LEU	PRO	ClinVar chr6:33408727	rs1761021165	Pathogenic/Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
627_LYS	THR	ClinVar chr6:33408961	rs1485749468	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
656_ASP	TYR	8.3kJPN chr6:33409047	-	-	0.0001	-
672_ARG	TER	ClinVar chr6:33409095	rs1060503383	Pathogenic/Likely pathogenic	-	Intellectual disability, autosomal dominant 5\|not provided\|13 conditions\|See cases [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621\|MedGen:C3661900\|13 conditions\|]
676_THR	PRO	ClinVar chr6:33409107	rs1581992998	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
681_LEU	PRO	ClinVar chr6:33409123	rs2151182679	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
682_TRP	TER	ClinVar chr6:33409126	-	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
687_GLN	TER	ClinVar chr6:33409140	rs1554121861	Pathogenic	-	not provided [MedGen:CN517202]
690_LYS	ASN	ClinVar chr6:33409151	rs1057518786	Likely pathogenic	-	not provided [MedGen:C3661900]
700_PRO	SER	ClinVar chr6:33409385	-	Likely pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]
701_ARG	GLN	ClinVar chr6:33409389	rs1060503384	Pathogenic	-	Intellectual disability, autosomal dominant 5 [MONDO:MONDO:0012960,MedGen:C2675473,OMIM:612621]

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