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NC_000014.8:g.(?_77743719)_(78082922_?)del AND Neuropathy, hereditary sensory and autonomic, type 1C

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 22, 2022
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:
RCV001996609.5

Allele description [Variation Report for NC_000014.8:g.(?_77743719)_(78082922_?)del]

NC_000014.8:g.(?_77743719)_(78082922_?)del

Genes:
  • NOXRED1:NADP dependent oxidoreductase domain containing 1 [Gene - HGNC]
  • VIPAS39:VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog [Gene - OMIM - HGNC]
  • AHSA1:activator of HSP90 ATPase activity 1 [Gene - OMIM - HGNC]
  • GSTZ1:glutathione S-transferase zeta 1 [Gene - OMIM - HGNC]
  • ISM2:isthmin 2 [Gene - OMIM - HGNC]
  • POMT2:protein O-mannosyltransferase 2 [Gene - OMIM - HGNC]
  • SPTLC2:serine palmitoyltransferase long chain base subunit 2 [Gene - OMIM - HGNC]
  • SAMD15:sterile alpha motif domain containing 15 [Gene - HGNC]
  • TMED8:transmembrane p24 trafficking protein family member 8 [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
14q24.3
Genomic location:
Chr14: 77743719 - 78082922 (on Assembly GRCh37)
Preferred name:
NC_000014.8:g.(?_77743719)_(78082922_?)del
HGVS:
NC_000014.8:g.(?_77743719)_(78082922_?)del

Condition(s)

Name:
Neuropathy, hereditary sensory and autonomic, type 1C
Synonyms:
HSAN IC; HSN IC; Hereditary sensory and autonomic neuropathy type IC
Identifiers:
MONDO: MONDO:0013337; MedGen: C3150896; Orphanet: 36386; OMIM: 613640

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002222770Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002222770.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with SPTLC2-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the SPTLC2 gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in SPTLC2 cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 9, 2024