Total 106 pathogenic variants reported for Coffin-Lowry syndrome 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_004586.3(RPS6KA3):c.224G>T (p.Gly75Val) SNV
Germline		 ChrX:20209307 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA255955 rs_122454124

1 SubmittersRCV000012417
NM_004586.3(RPS6KA3):c.679T>G (p.Ser227Ala) SNV
Germline		 ChrX:20187923 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA255956 rs_122454125

1 SubmittersRCV000012418
NM_004586.3(RPS6KA3):c.244G>T (p.Val82Phe) SNV
Germline		 ChrX:20204103 Pathogenic Coffin-Lowry syndrome
Thyroid cancer, nonmedullary, 1		 No Assertion Criteria Provided
 CA255957 rs_122454126

2 SubmittersRCV000012419RCV005887451
NM_004586.3(RPS6KA3):c.326-1G>C SNV
Unknown		 ChrX:20195146 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA255958 rs_587776755

1 SubmittersRCV000012420
NM_004586.3(RPS6KA3):c.340C>T (p.Arg114Trp) SNV
Germline		 ChrX:20195131 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA255959 rs_122454127

2 SubmittersRCV000012421
NM_004586.3(RPS6KA3):c.2065C>T (p.Gln689Ter) SNV
Germline		 ChrX:20156144 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA255960 rs_122454128

1 SubmittersRCV000012423
NM_004586.3(RPS6KA3):c.2186G>A (p.Arg729Gln) SNV
Germline		 ChrX:20155435 Pathogenic/Likely pathogenic Coffin-Lowry syndrome
Condition: not provided
Intellectual disability
Inborn genetic diseases
Nonpapillary renal cell carcinoma
Thyroid cancer, nonmedullary, 1
Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA255962 rs_28935171

7 SubmittersRCV000012424RCV000413967RCV001257622RCV001266366RCV005887452RCV005887453RCV006555318
NM_004586.3(RPS6KA3):c.566T>A (p.Ile189Lys) SNV
Germline		 ChrX:20193514 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA255963 rs_122454130

1 SubmittersRCV000012426
NM_004586.3(RPS6KA3):c.486+3A>G SNV
Germline		 ChrX:20194186 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA913185056 rs_1603426293

1 SubmittersRCV000012427
NM_004586.3(RPS6KA3):c.1000-2A>G SNV
Germline		 ChrX:20176354 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA412518051 rs_2148664125

1 SubmittersRCV000012430
NM_004586.3(RPS6KA3):c.803T>C (p.Phe268Ser) SNV
Germline		 ChrX:20186338 Pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA255964 rs_122454131

1 SubmittersRCV000012432
NM_004586.3(RPS6KA3):c.632-1G>C SNV
Germline		 ChrX:20187971 Pathogenic/Likely pathogenic Condition: not provided
Coffin-Lowry syndrome
Inborn genetic diseases		 Criteria Provided
Multiple Submitters
No Conflicts
 CA222782 rs_398124177

3 SubmittersRCV000081156RCV000760975RCV002514431
NM_004586.3(RPS6KA3):c.913C>T (p.Arg305Ter) SNV
Germline		 ChrX:20177017 Pathogenic Coffin-Lowry syndrome
Coffin-Lowry syndrome
Intellectual disability, X-linked 19
Condition: not provided
Thyroid cancer, nonmedullary, 1		 Criteria Provided
Multiple Submitters
No Conflicts
 CA358896 rs_869320705

6 SubmittersRCV000210889RCV000760245RCV004701277RCV005893891
NM_004586.3(RPS6KA3):c.1894C>T (p.Arg632Ter) SNV
Germline		 ChrX:20161709 Pathogenic Condition: not provided
Coffin-Lowry syndrome
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412513571 rs_1085307639

7 SubmittersRCV000489984RCV001249648RCV002523411
NM_004586.3(RPS6KA3):c.225G>T (p.Gly75=) SNV
Germline		 ChrX:20209306 Conflicting classifications of pathogenicity not specified
Intellectual disability, X-linked 19
Coffin-Lowry syndrome
RPS6KA3-related disorder
Ovarian serous cystadenocarcinoma		 Criteria Provided
Conflicting Classifications
 CA515613166 rs_1555950495

4 SubmittersRCV000502004RCV003766849RCV004737577RCV005899899
NM_004586.3(RPS6KA3):c.1762G>C (p.Glu588Gln) SNV
Germline		 ChrX:20164901 Likely pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA412513996 rs_1555927532

1 SubmittersRCV000505211
NM_004586.3(RPS6KA3):c.1699C>T (p.Gln567Ter) SNV
Germline		 ChrX:20164964 Pathogenic Inborn genetic diseases
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412514136 rs_1555927554

2 SubmittersRCV000624151RCV006556456
NM_004586.3(RPS6KA3):c.326-11A>G SNV
Germline		 ChrX:20195156 Conflicting classifications of pathogenicity Inborn genetic diseases
Coffin-Lowry syndrome
Condition: not provided
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Conflicting Classifications
 CA658799621 rs_1555943503

5 SubmittersRCV000623700RCV001798931RCV004702205RCV006556459
NM_004586.3(RPS6KA3):c.646A>G (p.Lys216Glu) SNV
Germline		 ChrX:20187956 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412508620 rs_1555939456

1 SubmittersRCV000625970
NM_004586.3(RPS6KA3):c.2185C>T (p.Arg729Trp) SNV
Germline		 ChrX:20155436 Pathogenic/Likely pathogenic Intellectual disability, X-linked 19
Coffin-Lowry syndrome
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412511813 rs_1555924331

5 SubmittersRCV000714792RCV000660251RCV003140055
NM_004586.3(RPS6KA3):c.1308C>A (p.Cys436Ter) SNV
Germline		 ChrX:20172791 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412516189 rs_1160828151

1 SubmittersRCV000660249
NM_004586.3(RPS6KA3):c.774+1G>C SNV
Germline		 ChrX:20187827 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412507923 rs_1555939331

1 SubmittersRCV000660247
NM_004586.3(RPS6KA3):c.334C>T (p.Arg112Ter) SNV
Germline		 ChrX:20195137 Pathogenic Coffin-Lowry syndrome
Condition: not provided
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412511061 rs_1555943479

4 SubmittersRCV000660245RCV004696969RCV005223090
NM_004586.3(RPS6KA3):c.328C>T (p.Arg110Ter) SNV
Germline		 ChrX:20195143 Pathogenic Coffin-Lowry syndrome
Condition: not provided
Intellectual disability		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412511086 rs_1555943484

3 SubmittersRCV000660244RCV001796175RCV001257663
NM_004586.3(RPS6KA3):c.629C>T (p.Thr210Ile) SNV
Unknown		 ChrX:20188499 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412508767 rs_1325953089

1 SubmittersRCV000677731
NM_004586.3(RPS6KA3):c.1603-5A>G SNV
Germline		 ChrX:20165065 Pathogenic/Likely pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA891843551 rs_1569194162

3 SubmittersRCV000702364RCV001784342
NM_004586.3(RPS6KA3):c.649G>A (p.Glu217Lys) SNV
Germline		 ChrX:20187953 Likely pathogenic Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Single Submitter
 CA412508603 rs_1569216119

1 SubmittersRCV000760275
NM_004586.3(RPS6KA3):c.932T>G (p.Leu311Ter) SNV
Germline		 ChrX:20176998 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412518228 rs_1603422403

1 SubmittersRCV000789047
NM_004586.3(RPS6KA3):c.1996C>T (p.Gln666Ter) SNV
Germline		 ChrX:20156213 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Single Submitter
 CA412512720 rs_1603417440

2 SubmittersRCV000808543RCV001535695
NM_004586.3(RPS6KA3):c.727C>T (p.Arg243Ter) SNV
Germline		 ChrX:20187875 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19
Condition: not provided
Coffin-Lowry syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412508173 rs_1603425345

3 SubmittersRCV000807329RCV003442092RCV005870896
NM_004586.3(RPS6KA3):c.748G>A (p.Asp250Asn) SNV
Germline		 ChrX:20187854 Conflicting classifications of pathogenicity Coffin-Lowry syndrome
Condition: not provided
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA412508072 rs_1603425338

3 SubmittersRCV000990500RCV003132131RCV002550619
NM_004586.3(RPS6KA3):c.243+1G>A SNV
Unknown		 ChrX:20209287 Pathogenic Coffin-Lowry syndrome
Thyroid cancer, nonmedullary, 1		 Criteria Provided
Single Submitter
 CA412512743 rs_1603428228

2 SubmittersRCV000990501RCV005912177
NM_004586.3(RPS6KA3):c.407-4T>G SNV
Germline		 ChrX:20194272 Conflicting classifications of pathogenicity Hirsutism
Motor delay
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Conflicting Classifications
 CA327476260 rs_1040089025

2 SubmittersRCV001007899RCV002068807
NM_004586.3(RPS6KA3):c.898C>T (p.Arg300Ter) SNV
Germline		 ChrX:20177032 Pathogenic Condition: not provided
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412518306 rs_1603422409

2 SubmittersRCV001007968RCV002549278
NM_004586.3(RPS6KA3):c.1765-2A>C SNV
Germline		 ChrX:20163042 Pathogenic Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Single Submitter
 CA412513983 rs_2067343280

1 SubmittersRCV001216393
NM_004586.3(RPS6KA3):c.1823T>G (p.Leu608Arg) SNV
Somatic		 ChrX:20162982 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412513742 rs_2067342745

1 SubmittersRCV001250664
NM_004586.3(RPS6KA3):c.212T>G (p.Leu71Ter) SNV
Germline		 ChrX:20209319 Pathogenic/Likely pathogenic Coffin-Lowry syndrome
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412512919 rs_2068650679

2 SubmittersRCV001251296RCV001819956
NM_004586.3(RPS6KA3):c.1507G>C (p.Asp503His) SNV
Unknown		 ChrX:20167684 Likely pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA412514868 rs_2067475470

1 SubmittersRCV001252610
NM_004586.3(RPS6KA3):c.432T>G (p.Tyr144Ter) SNV
Germline		 ChrX:20194243 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412510384 rs_2148701884

1 SubmittersRCV001376010
NM_004586.3(RPS6KA3):c.1376A>T (p.Asp459Val) SNV
Germline		 ChrX:20169469 Likely pathogenic Coffin-Lowry syndrome No Assertion Criteria Provided
 CA412515480 rs_2148653302

1 SubmittersRCV001528143
NM_004586.3(RPS6KA3):c.443A>T (p.Asp148Val) SNV
Germline		 ChrX:20194232 Likely pathogenic Coffin-Lowry syndrome
Thyroid cancer, nonmedullary, 1		 No Assertion Criteria Provided
 CA412510337 rs_2148701829

2 SubmittersRCV001528116RCV005911370
NM_004586.3(RPS6KA3):c.48G>C (p.Glu16Asp) SNV
Germline		 ChrX:20266585 Conflicting classifications of pathogenicity Condition: not provided
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Conflicting Classifications
 CA412510513 rs_1327104134

2 SubmittersRCV001596171RCV003771804
NM_004586.3(RPS6KA3):c.1661C>T (p.Pro554Leu) SNV
Germline		 ChrX:20165002 Conflicting classifications of pathogenicity Condition: not provided
Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Conflicting Classifications
 CA412514224 rs_2148643592

2 SubmittersRCV001665146RCV005213553
NM_004586.3(RPS6KA3):c.137G>A (p.Ser46Asn) SNV
Germline		 ChrX:20209394 Conflicting classifications of pathogenicity Condition: not provided
Inborn genetic diseases
Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Conflicting Classifications
 CA412513309 rs_1187541060

3 SubmittersRCV001765220RCV002540239RCV005225463
NM_004586.3(RPS6KA3):c.632-2A>C SNV
Germline		 ChrX:20187972 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412508692 rs_2148686736

1 SubmittersRCV001806395
NM_004586.3(RPS6KA3):c.1362T>G (p.Asp454Glu) SNV
Germline		 ChrX:20169483 Conflicting classifications of pathogenicity Coffin-Lowry syndrome
Intellectual disability, X-linked 19
Condition: not provided
RPS6KA3-related disorder		 Criteria Provided
Conflicting Classifications
 CA10366115 rs_762253691

3 SubmittersRCV002040590RCV003134349RCV004553631
NM_004586.3(RPS6KA3):c.17T>C (p.Leu6Pro) SNV
Germline		 ChrX:20266616 Conflicting classifications of pathogenicity Intellectual disability, X-linked 19
Coffin-Lowry syndrome
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA412510820 rs_1429116502

2 SubmittersRCV002090923RCV003149016
NM_004586.3(RPS6KA3):c.845+5G>A SNV
Germline		 ChrX:20186291 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Single Submitter
 CA2580100444 rs_2519725480

1 SubmittersRCV003041427
NM_004586.3(RPS6KA3):c.1814G>A (p.Gly605Asp) SNV
Germline		 ChrX:20162991 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Single Submitter
 CA412513761 rs_2519612941

1 SubmittersRCV002914310
NM_004586.3(RPS6KA3):c.83T>C (p.Ile28Thr) SNV
Germline		 ChrX:20234801 Conflicting classifications of pathogenicity Coffin-Lowry syndrome
Intellectual disability, X-linked 19
RPS6KA3-related disorder
not specified		 Criteria Provided
Conflicting Classifications
 CA10366346 rs_756013694

3 SubmittersRCV002995140RCV004550331RCV006460351
NM_004586.3(RPS6KA3):c.709C>T (p.Pro237Ser) SNV
Germline		 ChrX:20187893 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Single Submitter
 CA412508264 rs_2519732229

1 SubmittersRCV003045421
NM_004586.3(RPS6KA3):c.2101-2A>G SNV
Germline		 ChrX:20155522 Pathogenic Coffin-Lowry syndrome
Thyroid cancer, nonmedullary, 1
Nonpapillary renal cell carcinoma		 Criteria Provided
Single Submitter
 CA412512179 rs_2519568342

2 SubmittersRCV003223525RCV005930774RCV005930773
NM_004586.3(RPS6KA3):c.407-1G>T SNV
Germline		 ChrX:20194269 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412510486 rs_2519759849

1 SubmittersRCV003233428
NM_004586.3(RPS6KA3):c.406+1G>T SNV
Germline		 ChrX:20195064 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412510638 rs_2519762863

1 SubmittersRCV003322706
NM_004586.3(RPS6KA3):c.1540C>T (p.Arg514Ter) SNV
Germline		 ChrX:20167651 Pathogenic Condition: not provided
RPS6KA3-related disorder
Coffin-Lowry syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA412514787 rs_2519640130

3 SubmittersRCV004719325RCV004548636RCV004594694
NM_004586.3(RPS6KA3):c.1483C>A (p.Leu495Ile) SNV
Germline		 ChrX:20167708 Conflicting classifications of pathogenicity Coffin-Lowry syndrome
Intellectual disability, X-linked 19
RPS6KA3-related disorder
Coffin-Lowry syndrome		 Criteria Provided
Conflicting Classifications
 CA327474370 rs_937495958

3 SubmittersRCV003789693RCV004736661RCV003989863
NM_004586.3(RPS6KA3):c.955G>T (p.Glu319Ter) SNV
Germline		 ChrX:20176478 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Single Submitter
 CA412518166 rs_2519683509

1 SubmittersRCV003807460
NM_004586.3(RPS6KA3):c.244-1G>A SNV
Unknown		 ChrX:20204104 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 CA412511884 rs_2519798151

1 SubmittersRCV004006221
NM_004586.3(RPS6KA3):c.697G>T (p.Glu233Ter) SNV
Germline		 ChrX:20187905 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 rs_2519732291

2 SubmittersRCV004566622
NM_004586.3(RPS6KA3):c.602T>C (p.Leu201Pro) SNV
Germline		 ChrX:20188526 Pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter
 rs_2519735957

1 SubmittersRCV004594999
NM_004586.3(RPS6KA3):c.914G>A (p.Arg305Gln) SNV
Germline		 ChrX:20177016 Conflicting classifications of pathogenicity Condition: not provided
Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Conflicting Classifications

2 SubmittersRCV004727703RCV006565167
NM_004586.3(RPS6KA3):c.637G>T (p.Gly213Cys) SNV
Germline		 ChrX:20187965 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter

1 SubmittersRCV004759486
NM_004586.3(RPS6KA3):c.594T>G (p.Asn198Lys) SNV
Germline		 ChrX:20188534 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter

1 SubmittersRCV004789919
NM_004586.3(RPS6KA3):c.1354-12T>G SNV
Germline		 ChrX:20169503 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter

1 SubmittersRCV004799658
NM_004586.3(RPS6KA3):c.755G>A (p.Trp252Ter) SNV
Germline		 ChrX:20187847 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Single Submitter

1 SubmittersRCV005217372
NM_004586.3(RPS6KA3):c.283C>T (p.Gln95Ter) SNV
Germline		 ChrX:20204064 Pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19
Thyroid cancer, nonmedullary, 1		 Criteria Provided
Single Submitter

2 SubmittersRCV005214806RCV005939529
NM_004586.3(RPS6KA3):c.1740C>A (p.Tyr580Ter) SNV
Germline		 ChrX:20164923 Pathogenic Intellectual disability, X-linked 19
Coffin-Lowry syndrome		 Criteria Provided
Single Submitter

1 SubmittersRCV005218238
NM_004586.3(RPS6KA3):c.356G>A (p.Arg119His) SNV
Germline		 ChrX:20195115 Likely pathogenic Coffin-Lowry syndrome Criteria Provided
Single Submitter

1 SubmittersRCV005882665
NM_004586.3(RPS6KA3):c.594-1G>A SNV
Germline		 ChrX:20188535 Likely pathogenic Coffin-Lowry syndrome
Intellectual disability, X-linked 19		 Criteria Provided
Single Submitter

1 SubmittersRCV006591323