NM_006415.4(SPTLC1):c.112CTT[1] (p.Leu39del) AND Neuropathy, hereditary sensory and autonomic, type 1A

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: May 28, 2019
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000988188.5

Allele description [Variation Report for NM_006415.4(SPTLC1):c.112CTT[1] (p.Leu39del)]

NM_006415.4(SPTLC1):c.112CTT[1] (p.Leu39del)

Gene:

SPTLC1:serine palmitoyltransferase long chain base subunit 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9q22.31

Genomic location:

Preferred name:

NM_006415.4(SPTLC1):c.112CTT[1] (p.Leu39del)

HGVS:

NC_000009.12:g.92112503AAG[1]
NC_000009.12:g.92112503_92112505AAG[1]
NG_007950.1:g.7901CTT[1]
NM_001281303.2:c.112CTT[1]
NM_001368272.1:c.-388CTT[1]
NM_001368273.1:c.-354CTT[1]
NM_006415.4:c.112CTT[1]MANE SELECT
NM_178324.3:c.112CTT[1]
NP_001268232.1:p.Leu39del
NP_006406.1:p.Leu39del
NP_847894.1:p.Leu39del
LRG_272t1:c.115_117del
LRG_272:g.7901CTT[1]
NC_000009.11:g.94874785AAG[1]
NC_000009.11:g.94874785_94874787del
NC_000009.11:g.94874785_94874787delAAG
NM_006415.2:c.115_117delCTT
NM_006415.4:c.115_117delMANE SELECT
NM_006415.4:c.115_117delCTTMANE SELECT

Protein change:

L39del

Links:

OMIM: 605712.0010; dbSNP: rs1197928094

NCBI 1000 Genomes Browser:

rs1197928094

Molecular consequence:

NM_001368272.1:c.-388CTT[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001368273.1:c.-354CTT[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001281303.2:c.112CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_006415.4:c.112CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_178324.3:c.112CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Neuropathy, hereditary sensory and autonomic, type 1A (HSAN1A)
Synonyms:: NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IA; HSAN IA; HSN IA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008086; MedGen: C5235211; OMIM: 162400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001137822	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely pathogenic (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV005200025	Solve-RD Consortium	no assertion criteria provided	Likely pathogenic (Jun 1, 2022)	inherited	provider interpretation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001137822

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Likely pathogenic
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV005200025

Solve-RD Consortium

no assertion criteria provided

Likely pathogenic
(Jun 1, 2022)

inherited

provider interpretation

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	provider interpretation

Citations

PubMed

Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses.

Laurie S, Steyaert W, de Boer E, Polavarapu K, Schuermans N, Sommer AK, Demidov G, Ellwanger K, Paramonov I, Thomas C, Aretz S, Baets J, Benetti E, Bullich G, Chinnery PF, Clayton-Smith J, Cohen E, Danis D, de Sainte Agathe JM, Denommé-Pichon AS, Diaz-Manera J, Efthymiou S, et al.

Nat Med. 2025 Feb;31(2):478-489. doi: 10.1038/s41591-024-03420-w. Epub 2025 Jan 17.

PubMed [citation]

PMID:: 39825153
PMCID:: PMC11835725

Details of each submission

From Mendelics, SCV001137822.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Solve-RD Consortium, SCV005200025.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	provider interpretation	PubMed (1)

Description

Variant confirmed as disease-causing by referring clinical team

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 25, 2025

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