Total 108 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
Phelan-McDermid syndrome
Schizophrenia 15
Condition: not provided
Inborn genetic diseases
SHANK3-related disorder		 Criteria Provided
Conflicting Classifications
 CA10325937 rs_530255181

6 SubmittersRCV000239320RCV000765658RCV001711795RCV002313967RCV004734895
NM_001372044.2(SHANK3):c.2838C>G 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 Condition: not provided
Phelan-McDermid syndrome
Inborn genetic diseases
Intellectual disability
Neurodevelopmental abnormality		 Criteria Provided
Multiple Submitters
No Conflicts
 CA640057574 rs_1396379503

17 SubmittersRCV000658946RCV000850601RCV002315983RCV005626142RCV005235459
NM_001372044.2(SHANK3):c.496C>T (p.Arg166Ter) SNV
Germline		 Chr22:50676625 Pathogenic/Likely pathogenic Condition: not provided
Global developmental delay
Seizure
Inborn genetic diseases
Phelan-McDermid syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA515251897 rs_1569097392

4 SubmittersRCV000760828RCV001003640RCV002312264RCV006699323
NM_001372044.2(SHANK3):c.4978G>T (p.Glu1660Ter) SNV
Germline		 Chr22:50730869 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515266705 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
 CA915952297 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
 CA515264769 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
 CA10326125 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
 CA10326066 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
 CA515267138 rs_2083360139

1 SubmittersRCV001251636
NM_001372044.2(SHANK3):c.4690G>T (p.Asp1564Tyr) SNV
Germline		 Chr22:50722298 Pathogenic Phelan-McDermid syndrome Criteria Provided
Multiple Submitters
No Conflicts
 CA515265078 rs_373588048

2 SubmittersRCV001253156
NM_001372044.2(SHANK3):c.5209C>T (p.Gln1737Ter) SNV
Germline		 Chr22:50731100 Pathogenic/Likely pathogenic Autistic behavior
Condition: not provided
Phelan-McDermid syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA515267568 rs_1294272918

3 SubmittersRCV001281083RCV003321820RCV005055396
NM_001372044.2(SHANK3):c.1871G>C (p.Arg624Pro) SNV
Unknown		 Chr22:50703893 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515255793 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
 CA515252475 rs_2082934908

1 SubmittersRCV001330232
NM_001372044.2(SHANK3):c.4090C>T (p.Gln1364Ter) SNV
Germline		 Chr22:50721698 Pathogenic Condition: not provided
Phelan-McDermid syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA325579586 rs_1038102194

4 SubmittersRCV001529701RCV005253852
NM_001372044.2(SHANK3):c.4732C>T (p.Gln1578Ter) SNV
Germline		 Chr22:50722340 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515265240 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
 CA515254545 rs_200400333

1 SubmittersRCV001706756
NM_001372044.2(SHANK3):c.1336C>T (p.Gln446Ter) SNV
Germline		 Chr22:50694855 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515252351 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
 CA515259386 rs_2518425257

1 SubmittersRCV002287586
NM_001372044.2(SHANK3):c.4908C>G (p.Tyr1636Ter) SNV
Germline		 Chr22:50730799 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515266501 rs_2518438901

1 SubmittersRCV002466368
NM_001372044.2(SHANK3):c.1294C>T (p.Arg432Ter) SNV
Germline		 Chr22:50694813 Conflicting classifications of pathogenicity Phelan-McDermid syndrome
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA515252231 rs_2518393305

2 SubmittersRCV002795913RCV004774735
NM_001372044.2(SHANK3):c.800G>A (p.Arg267His) SNV
Germline		 Chr22:50678895 Conflicting classifications of pathogenicity Phelan-McDermid syndrome
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA10325265 rs_370831167

2 SubmittersRCV003136674RCV006651352
NM_001372044.2(SHANK3):c.3568C>T (p.Arg1190Ter) SNV
Germline		 Chr22:50721176 Conflicting classifications of pathogenicity Phelan-McDermid syndrome
not specified		 Criteria Provided
Conflicting Classifications
 CA515261368 rs_929358843

2 SubmittersRCV003149121RCV005927101
NM_001372044.2(SHANK3):c.4396G>T (p.Glu1466Ter) SNV
Germline		 Chr22:50722004 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515264167 rs_2518429961

1 SubmittersRCV003444184
NM_001372044.2(SHANK3):c.4987G>T (p.Glu1663Ter) SNV
Germline		 Chr22:50730878 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter
 CA515266732 rs_2518439090

1 SubmittersRCV003885401
NM_001372044.2(SHANK3):c.4910C>A (p.Ser1637Ter) SNV
Germline		 Chr22:50730801 Pathogenic Schizophrenia 15
Phelan-McDermid syndrome		 Criteria Provided
Single Submitter
 CA515266505 rs_1064796872

1 SubmittersRCV004006242
NM_001372044.2(SHANK3):c.2301-2A>T SNV
Germline		 Chr22:50711613 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV004699155
NM_001372044.2(SHANK3):c.676-2A>T SNV
Germline		 Chr22:50678767 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV005230898
NM_001372044.2(SHANK3):c.2540+2T>C SNV
Germline		 Chr22:50715755 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV005410881
NM_001372044.2(SHANK3):c.3094C>T (p.Gln1032Ter) SNV
Germline		 Chr22:50720702 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV005621358
NM_001372044.2(SHANK3):c.3835C>T (p.Gln1279Ter) SNV
Germline		 Chr22:50721443 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV005880731
NM_001372044.2(SHANK3):c.1191-1G>A SNV
Germline		 Chr22:50684584 Likely pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV006646677
NM_001372044.2(SHANK3):c.3529C>T (p.Leu1177=) SNV
Germline		 Chr22:50721137 Pathogenic Phelan-McDermid syndrome Criteria Provided
Single Submitter

1 SubmittersRCV006705220