NM_024589.3(ROGDI):c.695dup (p.Glu233fs) AND Amelocerebrohypohidrotic syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 12, 2021
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:: RCV002890942.3

Allele description [Variation Report for NM_024589.3(ROGDI):c.695dup (p.Glu233fs)]

NM_024589.3(ROGDI):c.695dup (p.Glu233fs)

Gene:

ROGDI:rogdi atypical leucine zipper [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_024589.3(ROGDI):c.695dup (p.Glu233fs)

HGVS:

NC_000016.10:g.4797939dup
NG_032174.1:g.10013dup
NM_024589.3:c.695dupMANE SELECT
NP_078865.1:p.Glu233Argfs
NP_078865.1:p.Glu233fs
LRG_455t1:c.694dup
LRG_455:g.10013dup
LRG_455p1:p.Glu233Argfs
NC_000016.9:g.4847938_4847939insA
NC_000016.9:g.4847940dup
NM_024589.2:c.694dup
NR_046480.2:n.702dup

Protein change:

E233fs

Molecular consequence:

NM_024589.3:c.695dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_046480.2:n.702dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Amelocerebrohypohidrotic syndrome (KTZS)
Synonyms:: EPILEPSY, DEMENTIA, AND AMELOGENESIS IMPERFECTA; Kohlschutter Tonz syndrome; Epilepsy dementia amelogenesis imperfecta; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009185; MedGen: C0406740; Orphanet: 1946; OMIM: 226750

Recent activity

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AGENCOURT_103340765 NICHD_XGC_tropInt_62 Xenopus tropicalis cDNA clone IMAGE:895...
AGENCOURT_103340765 NICHD_XGC_tropInt_62 Xenopus tropicalis cDNA clone IMAGE:8957005 5', mRNA sequence
gi|126538590|gnl|dbEST|45056602|gb| 315.1|

Nucleotide
BJ077965 NIBB Mochii normalized Xenopus tailbud library Xenopus laevis cDNA clon...
BJ077965 NIBB Mochii normalized Xenopus tailbud library Xenopus laevis cDNA clone XL062k16 3', mRNA sequence
gi|17522881|gnl|dbEST|10542274|dbj| 965.1|

Nucleotide
JGI_CAAO6821.fwd NIH_XGC_tropTe5 Xenopus tropicalis cDNA clone IMAGE:7703524 5',...
JGI_CAAO6821.fwd NIH_XGC_tropTe5 Xenopus tropicalis cDNA clone IMAGE:7703524 5', mRNA sequence
gi|58729624|gnl|dbEST|27646785|gb|C 66.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003248053	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 12, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003248053

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 12, 2021)

germline

clinical testing

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV003248053.2

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

Description

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with ROGDI-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the ROGDI gene (p.Glu233Argfs*99). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 55 amino acid(s) of the ROGDI protein and extend the protein by 43 additional amino acid residues.

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

Last Updated: Sep 29, 2024

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