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NM_024306.5(FA2H):c.75_77del (p.Cys25del) AND Spastic paraplegia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 8, 2024
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:
RCV000233207.5

Allele description [Variation Report for NM_024306.5(FA2H):c.75_77del (p.Cys25del)]

NM_024306.5(FA2H):c.75_77del (p.Cys25del)

Genes:
LOC130059394:ATAC-STARR-seq lymphoblastoid silent region 7701 [Gene]
FA2H:fatty acid 2-hydroxylase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q23.1
Genomic location:
Preferred name:
NM_024306.5(FA2H):c.75_77del (p.Cys25del)
HGVS:
  • NC_000016.10:g.74774681_74774683del
  • NC_000016.9:g.74808577_74808579del
  • NG_017070.1:g.5151_5153del
  • NM_024306.5:c.75_77delMANE SELECT
  • NP_077282.3:p.Cys25del
  • NC_000016.9:g.74808577_74808579del
  • NC_000016.9:g.74808577_74808579delCAG
  • NC_000016.9:g.74808579_74808581del
  • NM_024306.4:c.75_77delCTG
Protein change:
C25del
Links:
dbSNP: rs878855082
NCBI 1000 Genomes Browser:
rs878855082
Molecular consequence:
  • NM_024306.5:c.75_77del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
Spastic paraplegia
Identifiers:
MedGen: C0037772; Human Phenotype Ontology: HP:0001258

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000290710Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 8, 2024) 		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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000290710.5

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

Description

This variant, c.75_77del, results in the deletion of 1 amino acid(s) of the FA2H protein (p.Cys25del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of hereditary spastic paraplegia (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 241465). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Sep 29, 2024