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NM_024306.5(FA2H):c.265C>T (p.Gln89Ter) AND Spastic paraplegia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 25, 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:
RCV003064356.2

Allele description [Variation Report for NM_024306.5(FA2H):c.265C>T (p.Gln89Ter)]

NM_024306.5(FA2H):c.265C>T (p.Gln89Ter)

Genes:
LOC130059393:ATAC-STARR-seq lymphoblastoid silent region 7700 [Gene]
FA2H:fatty acid 2-hydroxylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q23.1
Genomic location:
Preferred name:
NM_024306.5(FA2H):c.265C>T (p.Gln89Ter)
HGVS:
  • NC_000016.10:g.74774491G>A
  • NG_017070.1:g.5341C>T
  • NM_024306.5:c.265C>TMANE SELECT
  • NP_077282.3:p.Gln89Ter
  • NC_000016.9:g.74808389G>A
Protein change:
Q89*
Molecular consequence:
  • NM_024306.5:c.265C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003443659Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 25, 2022) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Defective FA2H leads to a novel form of neurodegeneration with brain iron accumulation (NBIA).

Kruer MC, Paisán-Ruiz C, Boddaert N, Yoon MY, Hama H, Gregory A, Malandrini A, Woltjer RL, Munnich A, Gobin S, Polster BJ, Palmeri S, Edvardson S, Hardy J, Houlden H, Hayflick SJ.

Ann Neurol. 2010 Nov;68(5):611-8. doi: 10.1002/ana.22122.

PubMed [citation]
PMID:
20853438
PMCID:
PMC6059612

Fatty acid 2-hydroxylase deficiency: clinical features and brain iron accumulation.

Pedroso JL, Handfas BW, Abrahão A, Kok F, Barsottini OG, Oliveira AS.

Neurology. 2015 Mar 3;84(9):960-1. doi: 10.1212/WNL.0000000000001316. No abstract available.

PubMed [citation]
PMID:
25732363
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003443659.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln89*) in the FA2H gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FA2H are known to be pathogenic (PMID: 20853438, 25496456, 25732363, 26344562). This premature translational stop signal has been observed in individual(s) with hereditary spastic paraplegia (PMID: 25496456). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 14, 2024