RGD:8596567 Rat Genome Database

Variant: RGD:8596567 - Homo sapiens

RGD ID:

8596567

RS ID:

rs119482084

ClinVar ID:

CV19841

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

SPTLC1

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	9	94,800,624
GRCh38	9	92,038,342

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

ClinVar Data

HGVS Name(s)	Last Evaluated	Molecular Consequence	Clinical Significance	Age of Onset	Trait Synonyms
LRG_272:g.82067G>C NG_007950.1:g.82067G>C NC_000009.12:g.92038342C>G NM_006415.2:c.1160G>C More...	06/01/2023	missense\|missense variant	pathogenic\|benign\|likely benign\|conflicting interpretations of pathogenicity\|uncertain significance	all ages\|variable	Charcot-Marie-Tooth Neuropathy; Hereditary sensory neuropathy type 1; Hereditary Sensory Neuropathy Type I; Hereditary Sensory Neuropathy Type IA; HSAN 1; HSAN IA; HSN IA; HSN Type I; Neuropathy hereditary sensory radicular, autosomal dominant; NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IA; NEUROPATHY, HEREDITARY SENSORY RADICULAR, AUTOSOMAL DOMINANT, TYPE 1A; none provided

Disease Annotations Click to see Annotation Detail View

Charcot-Marie-Tooth disease (IAGP)

genetic disease (IAGP)

hereditary sensory and autonomic neuropathy type 1 (IAGP)

hereditary sensory and autonomic neuropathy type 1A (IAGP)

Variant Details

Variant Transcripts

Gene Symbol:	SPTLC1
Accession:	XM_047422638
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	326

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKNHLATLHLVIGESKLSIFKDIIKSPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGT FDVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLL KEQEIEDQKNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDID LISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGIS GLKVVAESLSPAFHLQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAA STIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	NM_006415
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	387

Amino Acid Sequence (Calculated using NCBI transcript definition)
MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPAL NYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEE AIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRR FIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIGGFCCG RSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVAESLSPAFHLQLEE STGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	XM_024447378
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	232

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKA RVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIG GFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVAESLSPAFH LQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	NM_001281303
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	387

Amino Acid Sequence (Calculated using NCBI transcript definition)
MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPAL NYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEE AIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRR FIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIGGFCCG RSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVAESLSPAFHLQLEE STGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPRGRTGESCVHHQGGSPGRPALGRVPGPWPPATQHAERT QDSRWPWSGLKESKNMWIFDRIVTKWCQYGPIV*

Gene Symbol:	SPTLC1
Accession:	XM_024447379
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	232

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKA RVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIG GFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVAESLSPAFH LQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	NM_001368272
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	265

Amino Acid Sequence (Calculated using NCBI transcript definition)
MYDFKYSEFPGSHQRRPAFYDVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQAS RSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVL GEHGRGVTEHYGINIDDIDLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGI FAVLKEKCGQIHKALQGISGLKVVAESLSPAFHLQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPP SIRVVVTVEQTEEELERAASTIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	NM_001368273
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	232

Amino Acid Sequence (Calculated using NCBI transcript definition)
MKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKA RVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDIDLISANMENALASIG GFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLKEKCGQIHKALQGISGLKVVAESLSPAFH LQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	XM_047422639
Location:	EXON
Amino Acid Prediction:	G to A (nonsynonymous)
Amino Acid Position:	260

Amino Acid Sequence (Calculated using NCBI transcript definition)
MDHTHRRYGHQKLKKNVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSKRGDIVFVDRAACFAIQKGLQASRSDIK LFKHNDMADLERLLKEQEIEDQKNPRKARVTRRFIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGR GVTEHYGINIDDIDLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENPGIFAVLK EKCGQIHKALQGISGLKVVAESLSPAFHLQLEESTGSREQDVRLLQEIVDQCMNRSIALTQARYLEKEEKCLPPPSIRVV VTVEQTEEELERAASTIKEVAQAVLL*

Gene Symbol:	SPTLC1
Accession:	NM_178324
Location:	INTRON

Variant Samples

ClinVar GRCh37

ClinVar GRCh38

Additional References at PubMed

PMID:13646503	PMID:15037712	PMID:19132419	PMID:20301564	PMID:25741868	PMID:26681808	PMID:28492532

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV000005069	CLINVAR
	RCV000789583	CLINVAR
	RCV001249812	CLINVAR
	RCV001310659	CLINVAR
	RCV002371761	CLINVAR
dbSNP (RS)	rs119482084	CLINVAR
MedGen	C0007959	CLINVAR
	C0020071	CLINVAR
	C0950123	CLINVAR
	C3661900	CLINVAR
	C5235211	CLINVAR
NCBI Gene	SPTLC1	CLINVAR
OMIM	162400	CLINVAR
	605712	CLINVAR
OMIM Allele	605712.0004	CLINVAR
SNOMED CT	50548001	CLINVAR

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Variant: RGD:8596567 - Homo sapiens

Imported Disease Annotations - ClinVar