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NM_014053.4(FLVCR1):c.1092+5G>A

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 24, 2021)
Last evaluated:
Oct 23, 2020
Accession:
VCV000374768.12
Variation ID:
374768
Description:
single nucleotide variant
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NM_014053.4(FLVCR1):c.1092+5G>A

Allele ID
361654
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q32.3
Genomic location
1: 212883443 (GRCh38) GRCh38 UCSC
1: 213056785 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.213056785G>A
NC_000001.11:g.212883443G>A
NG_028131.1:g.30189G>A
NM_014053.4:c.1092+5G>A MANE Select
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:212883442:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00030
Exome Aggregation Consortium (ExAC) 0.00023
The Genome Aggregation Database (gnomAD) 0.00032
The Genome Aggregation Database (gnomAD), exomes 0.00024
Links
ClinGen: CA1386046
dbSNP: rs556788423
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 5 criteria provided, multiple submitters, no conflicts Oct 23, 2020 RCV000415829.7
Likely pathogenic 1 criteria provided, single submitter May 28, 2019 RCV000986509.1
Pathogenic 1 criteria provided, single submitter Jun 25, 2019 RCV001075766.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FLVCR1 - - GRCh38
GRCh37
300 324

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 16, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000577806.5
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Reduces the quality of the splice donor site in intron 4, and an in vitro functional study suggests a damaging effect with abnormal splicing and … (more)
Pathogenic
(Sep 01, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000493676.11
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Posterior column ataxia-retinitis pigmentosa syndrome
Allele origin: unknown
Mendelics
Accession: SCV001135524.1
Submitted: (Oct 22, 2019)
Evidence details
Pathogenic
(Jun 25, 2019)
criteria provided, single submitter
Method: clinical testing
Retinal dystrophy
Allele origin: germline
Blueprint Genetics
Accession: SCV001241398.1
Submitted: (Oct 15, 2019)
Comment:
My Retina Tracker patient
Evidence details
Pathogenic
(Oct 29, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001409598.1
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change falls in intron 4 of the FLVCR1 gene. It does not directly change the encoded amino acid sequence of the FLVCR1 protein, … (more)
Pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
(Unknown mechanism)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001446625.1
Submitted: (Oct 23, 2020)
Evidence details
Likely pathogenic
(Oct 12, 2020)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001713133.1
Submitted: (May 26, 2021)
Evidence details
Publications
PubMed (8)
Comment:
PS3, PS4_moderate, PM2, PP3

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Findings from a Genotyping Study of Over 1000 People with Inherited Retinal Disorders in Ireland. Whelan L Genes 2020 PMID: 31963381
A Novel FLVCR1 Variant Implicated in Retinitis Pigmentosa. Dockery A Advances in experimental medicine and biology 2019 PMID: 31884612
Phenotypic spectrum of autosomal recessive retinitis pigmentosa without posterior column ataxia caused by mutations in the FLVCR1 gene. Kuehlewein L Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie 2019 PMID: 30656474
Unraveling the Role of Heme in Neurodegeneration. Chiabrando D Frontiers in neuroscience 2018 PMID: 30356807
A splice-site variant in FLVCR1 produces retinitis pigmentosa without posterior column ataxia. Yusuf IH Ophthalmic genetics 2018 PMID: 29192808
Posterior column ataxia with retinitis pigmentosa coexisting with sensory-autonomic neuropathy and leukemia due to the homozygous p.Pro221Ser FLVCR1 mutation. Castori M American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2017 PMID: 28766925
Next generation sequencing based identification of disease-associated mutations in Swiss patients with retinal dystrophies. Tiwari A Scientific reports 2016 PMID: 27353947
Panel-based next generation sequencing as a reliable and efficient technique to detect mutations in unselected patients with retinal dystrophies. Glöckle N European journal of human genetics : EJHG 2014 PMID: 23591405

Text-mined citations for rs556788423...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021