A total 34 pathogenic variants reported in gene serine palmitoyltransferase long chain base subunit 1 (SPTLC1)  
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_006415.4(SPTLC1):c.398G>A (p.Cys133Tyr) SNV
Germline		 Chr9:92080045 Pathogenic Hereditary sensory and autonomic neuropathy type 1
Charcot-Marie-Tooth disease
Neuropathy, hereditary sensory and autonomic, type 1A
Inborn genetic diseases
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA340286 rs_119482081

8 SubmittersRCV000005067RCV001027483RCV001249800RCV002512792RCV004998075
NM_006415.4(SPTLC1):c.431T>A (p.Val144Asp) SNV
Germline		 Chr9:92068095 Pathogenic/Likely pathogenic Hereditary sensory and autonomic neuropathy type 1
Condition: not provided
Neuropathy, hereditary sensory and autonomic, type 1A
Charcot-Marie-Tooth disease
Inborn genetic diseases
SPTLC1-related disorder
Amyotrophic lateral sclerosis 27, juvenile		 Criteria Provided
Multiple Submitters
No Conflicts
 CA340288 rs_119482083

12 SubmittersRCV000005068RCV000235837RCV001249799RCV001174070RCV002326664RCV004755711RCV006635410
NM_006415.4(SPTLC1):c.399T>G (p.Cys133Trp) SNV
Germline		 Chr9:92080044 Pathogenic Hereditary sensory and autonomic neuropathy type 1
Sensorimotor neuropathy
Neuropathy, hereditary sensory and autonomic, type 1A
Charcot-Marie-Tooth disease
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA340293 rs_119482082

6 SubmittersRCV000005070RCV001004021RCV001249798RCV001174071RCV004597725
NM_006415.4(SPTLC1):c.992C>T (p.Ser331Phe) SNV
Germline		 Chr9:92047261 Pathogenic Neuropathy, hereditary sensory and autonomic, type IA, severe
Neuropathy, hereditary sensory and autonomic, type 1A		 Criteria Provided
Single Submitter
 CA117094 rs_267607087

3 SubmittersRCV000005071RCV003223389
NM_006415.4(SPTLC1):c.1072G>C (p.Glu358Gln) SNV
Germline		 Chr9:92047181 Likely pathogenic Hereditary sensory and autonomic neuropathy type 1 Criteria Provided
Single Submitter
 CA276171 rs_797045071

1 SubmittersRCV000191132
NM_006415.4(SPTLC1):c.784A>G (p.Lys262Glu) SNV
Germline		 Chr9:92050064 Conflicting classifications of pathogenicity Condition: not provided
Hereditary sensory and autonomic neuropathy type 1
Inborn genetic diseases
not specified		 Criteria Provided
Conflicting Classifications
 CA5121423 rs_139086093

4 SubmittersRCV000219590RCV001854747RCV002408939RCV004800347
NM_006415.4(SPTLC1):c.208G>T (p.Val70Phe) SNV
Germline		 Chr9:92108792 Conflicting classifications of pathogenicity Condition: not provided
Hereditary sensory and autonomic neuropathy type 1
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA5121647 rs_764460003

4 SubmittersRCV000217685RCV000534413RCV000624408
NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser) SNV
Germline		 Chr9:92112562 Pathogenic Condition: not provided
Amyotrophic lateral sclerosis 27, juvenile
Neuropathy, hereditary sensory and autonomic, type 1A
Ritscher-Schinzel syndrome 4		 Criteria Provided
Multiple Submitters
No Conflicts
 CA10584304 rs_879254294

4 SubmittersRCV000236861RCV003223342RCV004594033RCV005860050
NM_006415.4(SPTLC1):c.58-9C>T SNV
Germline		 Chr9:92112571 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type 1A		 Criteria Provided
Conflicting Classifications
 CA5121683 rs_769188151

2 SubmittersRCV000277993RCV001249801
NM_006415.4(SPTLC1):c.640A>G (p.Met214Val) SNV
Germline		 Chr9:92059229 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type 1A		 Criteria Provided
Conflicting Classifications
 CA5121490 rs_781435924

2 SubmittersRCV000397298RCV001249804
NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr) SNV
Germline		 Chr9:92047261 Pathogenic Condition: not provided
Charcot-Marie-Tooth disease
Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type IA, severe
Amyotrophic lateral sclerosis 27, juvenile		 Criteria Provided
Multiple Submitters
No Conflicts
 CA16042656 rs_267607087

4 SubmittersRCV000414705RCV000790228RCV000795948RCV001249813RCV003152600
NM_006415.4(SPTLC1):c.1402G>T (p.Ala468Ser) SNV
Germline		 Chr9:92032485 Conflicting classifications of pathogenicity Condition: not provided
Hereditary sensory and autonomic neuropathy type 1
Charcot-Marie-Tooth disease
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA5121188 rs_748723735

5 SubmittersRCV000488106RCV000692000RCV001174084RCV002393027
NM_006415.4(SPTLC1):c.1329-9T>C SNV
Germline		 Chr9:92032567 Conflicting classifications of pathogenicity not specified
Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type 1A		 Criteria Provided
Conflicting Classifications
 CA5121215 rs_778388513

3 SubmittersRCV000424196RCV000560512RCV001249819
NM_006415.4(SPTLC1):c.120C>G (p.Phe40Leu) SNV
Germline		 Chr9:92112500 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type 1A
Charcot-Marie-Tooth disease
Condition: not provided
Inborn genetic diseases
not specified		 Criteria Provided
Conflicting Classifications
 CA5121677 rs_142153571

8 SubmittersRCV000871430RCV001249820RCV001174074RCV001722441RCV002358410RCV006452708
NM_006415.4(SPTLC1):c.68A>T (p.Tyr23Phe) SNV
Germline		 Chr9:92112552 Likely pathogenic Condition: not provided
Neuropathy, hereditary sensory and autonomic, type 1A
Amyotrophic lateral sclerosis 27, juvenile		 Criteria Provided
Multiple Submitters
No Conflicts
 CA373795895 rs_1554716504

3 SubmittersRCV000522579RCV001267702RCV003152607
NM_006415.4(SPTLC1):c.1015G>T (p.Ala339Ser) SNV
Germline		 Chr9:92047238 Pathogenic Hereditary sensory and autonomic neuropathy type 1 Criteria Provided
Single Submitter
 CA373792546 rs_1554706429

1 SubmittersRCV000557521
NM_006415.4(SPTLC1):c.1012T>A (p.Ser338Thr) SNV
Germline		 Chr9:92047241 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA373792554 rs_1554706430

2 SubmittersRCV000543042RCV002350177
NM_006415.4(SPTLC1):c.929C>G (p.Ala310Gly) SNV
Germline		 Chr9:92047668 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Charcot-Marie-Tooth disease
Neuropathy, hereditary sensory and autonomic, type 1A
not specified
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA5121379 rs_768841574

5 SubmittersRCV000631312RCV000790229RCV001249816RCV006459696RCV005429262
NM_006415.4(SPTLC1):c.1213C>T (p.Arg405Cys) SNV
Germline		 Chr9:92038289 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Inborn genetic diseases
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA5121281 rs_745684683

4 SubmittersRCV000631307RCV003352947RCV004691962
NM_006415.4(SPTLC1):c.1168C>T (p.Leu390Phe) SNV
Germline		 Chr9:92038334 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Charcot-Marie-Tooth disease
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA5121287 rs_369803886

3 SubmittersRCV000806535RCV001174080RCV002332649
NM_006415.4(SPTLC1):c.707G>C (p.Arg236Pro) SNV
Germline		 Chr9:92055478 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA5121458 rs_765970732

2 SubmittersRCV000814232RCV005492890
NM_006415.4(SPTLC1):c.388G>T (p.Val130Leu) SNV
Germline		 Chr9:92080055 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Charcot-Marie-Tooth disease		 Criteria Provided
Conflicting Classifications
 CA5121582 rs_200773661

2 SubmittersRCV000874259RCV001174078
NM_006415.4(SPTLC1):c.1111G>A (p.Gly371Arg) SNV
Germline		 Chr9:92046024 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type 1A
Amyotrophic lateral sclerosis 27, juvenile
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA5121315 rs_147143593

3 SubmittersRCV000907066RCV005392533RCV006442001
NM_006415.4(SPTLC1):c.165+4C>T SNV
Germline		 Chr9:92112451 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Neuropathy, hereditary sensory and autonomic, type 1A		 Criteria Provided
Conflicting Classifications
 CA5121669 rs_750680286

2 SubmittersRCV001067127RCV001249821
NM_006415.4(SPTLC1):c.367G>A (p.Ala123Thr) SNV
Germline		 Chr9:92080076 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Inborn genetic diseases
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA5121586 rs_748384890

3 SubmittersRCV001321679RCV002456439RCV004597982
NM_006415.4(SPTLC1):c.1393A>G (p.Lys465Glu) SNV
Germline		 Chr9:92032494 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Condition: not provided
Neuropathy, hereditary sensory and autonomic, type 1A
Amyotrophic lateral sclerosis 27, juvenile		 Criteria Provided
Conflicting Classifications
 CA5121190 rs_773640417

3 SubmittersRCV001346684RCV002276698RCV005361552
NM_006415.4(SPTLC1):c.1288C>T (p.Arg430Cys) SNV
Germline		 Chr9:92034850 Conflicting classifications of pathogenicity Condition: not provided
Hereditary sensory and autonomic neuropathy type 1		 Criteria Provided
Conflicting Classifications
 CA5121241 rs_143754785

2 SubmittersRCV001572255RCV002569058
NM_006415.4(SPTLC1):c.986G>A (p.Arg329Gln) SNV
Unknown		 Chr9:92047267 Likely pathogenic Neuropathy, hereditary sensory and autonomic, type 1A Criteria Provided
Single Submitter
 CA373792609 rs_2118448441

1 SubmittersRCV001754569
NM_006415.4(SPTLC1):c.940A>G (p.Ile314Val) SNV
Germline		 Chr9:92047657 Conflicting classifications of pathogenicity Hereditary sensory and autonomic neuropathy type 1
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA5121376 rs_199609730

2 SubmittersRCV001906681RCV006650971
NM_006415.4(SPTLC1):c.398G>T (p.Cys133Phe) SNV
Germline		 Chr9:92080045 Likely pathogenic Hereditary sensory and autonomic neuropathy type 1 Criteria Provided
Single Submitter
 CA373788049 rs_119482081

1 SubmittersRCV002601672
NM_006415.4(SPTLC1):c.113T>G (p.Leu38Arg) SNV
Germline		 Chr9:92112507 Pathogenic Amyotrophic lateral sclerosis 27, juvenile No Assertion Criteria Provided
 CA373795568 rs_1478177125

1 SubmittersRCV003152660