Total 67 pathogenic variants reported for Phelan-McDermid syndrome 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_001372044.2(SHANK3):c.646C>G (p.Pro216Ala) SNV
Germline		 Chr22:50678666 Likely pathogenic Phelan-McDermid syndrome
Condition: not provided		 Criteria Provided
Single Submitter
 CA263235 rs_397514705

2 SubmittersRCV000043655RCV001804766
NM_001372044.2(SHANK3):c.3133G>T (p.Ala1045Ser) SNV
Germline		 Chr22:50720741 Conflicting classifications of pathogenicity not specified
Schizophrenia 15
Phelan-McDermid syndrome
Condition: not provided
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA10325937 rs_530255181

5 SubmittersRCV000239320RCV000765658RCV001711795RCV002313967
NM_033517.1(SHANK3):c.2613C>G (p.Tyr871Ter) SNV
Germline		 Chr22:50720446 Pathogenic Condition: not provided
Phelan-McDermid syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA16043165 rs_1001153999

2 SubmittersRCV000412919RCV001823001
NM_001372044.2(SHANK3):c.1255G>T (p.Val419Leu) SNV
Germline		 Chr22:50684651 Likely pathogenic Phelan-McDermid syndrome No Assertion Criteria Provided
 CA16044390 rs_1057519406

1 SubmittersRCV000417108
NM_001372044.2(SHANK3):c.2455+1G>A SNV
Germline		 Chr22:50715048 Pathogenic/Likely pathogenic Condition: not provided
Phelan-McDermid syndrome
Inborn genetic diseases		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_1396379503

10 SubmittersRCV000658946RCV000850601RCV002315983
NM_001372044.2(SHANK3):c.4978G>T (p.Glu1660Ter) SNV
Germline		 Chr22:50730869 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_1603447380

1 SubmittersRCV000984485
NM_001372044.2(SHANK3):c.494+2T>G SNV
Unknown		 Chr22:50675253 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_1603445997

1 SubmittersRCV000990464
NM_001372044.2(SHANK3):c.4600G>A (p.Gly1534Arg) SNV
Germline		 Chr22:50722208 Conflicting classifications of pathogenicity Condition: not provided
Phelan-McDermid syndrome		 Criteria Provided
Conflicting Classifications
 rs_1440735830

2 SubmittersRCV000997958RCV003127574
NM_001372044.2(SHANK3):c.3985C>T (p.Pro1329Ser) SNV
Germline		 Chr22:50721593 Conflicting classifications of pathogenicity Phelan-McDermid syndrome
Condition: not provided		 Criteria Provided
Conflicting Classifications
 rs_748123356

2 SubmittersRCV001197699RCV002293507
NM_001372044.2(SHANK3):c.3777G>A (p.Glu1259=) SNV
Germline		 Chr22:50721385 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_763158627

1 SubmittersRCV001249902
NM_001372044.2(SHANK3):c.5107C>A (p.Arg1703Ser) SNV
Germline		 Chr22:50730998 Pathogenic Phelan-McDermid syndrome No Assertion Criteria Provided
 rs_2083360139

1 SubmittersRCV001251636
NM_001372044.2(SHANK3):c.4690G>T (p.Asp1564Tyr) SNV
Germline		 Chr22:50722298 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_373588048

1 SubmittersRCV001253156
NM_001372044.2(SHANK3):c.1871G>C (p.Arg624Pro) SNV
Unknown		 Chr22:50703893 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_2083140726

1 SubmittersRCV001291836
NM_001372044.2(SHANK3):c.574A>T (p.Lys192Ter) SNV
Unknown		 Chr22:50678594 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_2082934908

1 SubmittersRCV001330232
NM_001372044.2(SHANK3):c.4732C>T (p.Gln1578Ter) SNV
Germline		 Chr22:50722340 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_2146833747

1 SubmittersRCV001533003
NM_001372044.2(SHANK3):c.1065C>G (p.Asn355Lys) SNV
Unknown		 Chr22:50679383 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_200400333

1 SubmittersRCV001706756
NM_001372044.2(SHANK3):c.5160C>T (p.Pro1720=) SNV
Germline		 Chr22:50731051 Conflicting classifications of pathogenicity Condition: not provided
Phelan-McDermid syndrome
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 rs_751652089

4 SubmittersRCV001714909RCV001775182RCV002343801
NM_001372044.2(SHANK3):c.1336C>T (p.Gln446Ter) SNV
Germline		 Chr22:50694855 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 rs_2146794652

1 SubmittersRCV001785873
NM_001372044.2(SHANK3):c.2871T>A (p.Tyr957Ter) SNV
Germline		 Chr22:50720479 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV002287586
NM_001372044.2(SHANK3):c.4908C>G (p.Tyr1636Ter) SNV
Germline		 Chr22:50730799 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV002466368
NM_001372044.2(SHANK3):c.1294C>T (p.Arg432Ter) SNV
Germline		 Chr22:50694813 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV002795913
NM_001372044.2(SHANK3):c.3568C>T (p.Arg1190Ter) SNV
Germline		 Chr22:50721176 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV003149121
NM_001372044.2(SHANK3):c.4396G>T (p.Glu1466Ter) SNV
Germline		 Chr22:50722004 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV003444184
NM_001372044.2(SHANK3):c.4987G>T (p.Glu1663Ter) SNV
Germline		 Chr22:50730878 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV003885401
NM_001372044.2(SHANK3):c.4910C>A (p.Ser1637Ter) SNV
Germline		 Chr22:50730801 Pathogenic Phelan-McDermid syndrome
Schizophrenia 15		 Criteria Provided
Single Submitter

1 SubmittersRCV004006242