ClinVar Miner

List of variants in gene SPTLC1 reported as pathogenic for hereditary sensory and autonomic neuropathy

Included ClinVar conditions (44):

Autosomal dominant cerebellar ataxia, deafness and narcolepsy; Hereditary sensory neuropathy-deafness-dementia syndrome
Channelopathy-associated congenital insensitivity to pain, autosomal recessive
Charcot-Marie-Tooth disease X-linked recessive 4; Deafness, X-linked 5; Severe X-linked mitochondrial encephalomyopathy
Charcot-Marie-Tooth disease X-linked recessive 4; Deafness, X-linked 5; Spondyloepimetaphyseal dysplasia, Bieganski type; Severe X-linked mitochondrial encephalomyopathy
Cold-induced sweating syndrome
Cold-induced sweating syndrome 1
Cold-induced sweating syndrome 2
Congenital insensitivity to pain-hypohidrosis syndrome
Congenital sensory neuropathy with selective loss of small myelinated fibers
Deafness, X-linked 5
Hereditary insensitivity to pain with anhidrosis
Hereditary insensitivity to pain with anhidrosis; Familial medullary thyroid carcinoma
Hereditary sensory and autonomic neuropathy
Hereditary sensory and autonomic neuropathy type 1
Hereditary sensory and autonomic neuropathy type 2
Hereditary sensory and autonomic neuropathy type 6
Hereditary sensory and autonomic neuropathy type 6; Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency
Hereditary sensory and autonomic neuropathy type 7
Hereditary sensory and autonomic neuropathy type 7; Familial episodic pain syndrome with predominantly lower limb involvement
Hereditary sensory neuropathy-deafness-dementia syndrome
Hereditary spastic paraplegia 30; Neuropathy, hereditary sensory, type 2C
Hereditary spastic paraplegia 30; Neuropathy, hereditary sensory, type 2C; Intellectual disability, autosomal dominant 9
Hereditary spastic paraplegia 3A; Neuropathy, hereditary sensory, type 1D
Neuropathy, hereditary sensory and autonomic, type 1A
Neuropathy, hereditary sensory and autonomic, type 1C
Neuropathy, hereditary sensory and autonomic, type 2A
Neuropathy, hereditary sensory and autonomic, type 2A; Generalized epilepsy with febrile seizures plus, type 7
Neuropathy, hereditary sensory and autonomic, type 2A; Hereditary spastic paraplegia 30; Neuropathy, hereditary sensory, type 2C; Intellectual disability, autosomal dominant 9
Neuropathy, hereditary sensory and autonomic, type 2A; Neuropathy, hereditary sensory and autonomic, type 2B
Neuropathy, hereditary sensory and autonomic, type 2A; Pseudohypoaldosteronism type 2C
Neuropathy, hereditary sensory and autonomic, type 2B
Neuropathy, hereditary sensory, type 1D
Neuropathy, hereditary sensory, type 1F
Neuropathy, hereditary sensory, type 2C
PERCHING syndrome
PERCHING syndrome; Bohring-Opitz-like syndrome
Primary erythromelalgia; Neuropathy, hereditary sensory and autonomic, type 2A; Paroxysmal extreme pain disorder; Channelopathy-associated congenital insensitivity to pain, autosomal recessive
Primary erythromelalgia; Neuropathy, hereditary sensory and autonomic, type 2A; Paroxysmal extreme pain disorder; Channelopathy-associated congenital insensitivity to pain, autosomal recessive; Generalized epilepsy with febrile seizures plus
Primary erythromelalgia; Neuropathy, hereditary sensory and autonomic, type 2A; Paroxysmal extreme pain disorder; Channelopathy-associated congenital insensitivity to pain, autosomal recessive; Generalized epilepsy with febrile seizures plus, type 7
Primary erythromelalgia; Neuropathy, hereditary sensory and autonomic, type 2A; Paroxysmal extreme pain disorder; Generalized epilepsy with febrile seizures plus
Primary erythromelalgia; Neuropathy, hereditary sensory and autonomic, type 2A; Paroxysmal extreme pain disorder; Severe myoclonic epilepsy in infancy; Channelopathy-associated congenital insensitivity to pain, autosomal recessive; Generalized epilepsy with febrile seizures plus, type 7
Primary erythromelalgia; Paroxysmal extreme pain disorder; Channelopathy-associated congenital insensitivity to pain, autosomal recessive
Primary erythromelalgia; Paroxysmal extreme pain disorder; Severe myoclonic epilepsy in infancy; Channelopathy-associated congenital insensitivity to pain, autosomal recessive; Generalized epilepsy with febrile seizures plus, type 7
Retinitis pigmentosa; Hereditary sensory and autonomic neuropathy

Minimum submission review status:		Collection method:
Minimum conflict level: Report conflict between different conditions
Gene type: Distinguish antisense genes from sense genes
Show significances as they were submitted (without aggregation into standard terms)
		ClinVar version:

Total variants: 9

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HGVS	dbSNP	gnomAD frequency
NM_006415.4(SPTLC1):c.431T>A (p.Val144Asp)	rs119482083	0.00001
NM_006415.4(SPTLC1):c.1015G>T (p.Ala339Ser)	rs1554706429
NM_006415.4(SPTLC1):c.1055C>T (p.Ala352Val)	rs267607088
NM_006415.4(SPTLC1):c.112CTT[1] (p.Leu39del)	rs1197928094
NM_006415.4(SPTLC1):c.398G>A (p.Cys133Tyr)	rs119482081
NM_006415.4(SPTLC1):c.399T>G (p.Cys133Trp)	rs119482082
NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser)	rs879254294
NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr)	rs267607087
NM_006415.4(SPTLC1):c.992C>T (p.Ser331Phe)	rs267607087

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