NM_024589.3(ROGDI):c.692T>C (p.Met231Thr) AND Amelocerebrohypohidrotic syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 27, 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:: RCV001347281.7

Allele description [Variation Report for NM_024589.3(ROGDI):c.692T>C (p.Met231Thr)]

NM_024589.3(ROGDI):c.692T>C (p.Met231Thr)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_024589.3(ROGDI):c.692T>C (p.Met231Thr)

HGVS:

NC_000016.10:g.4797941A>G
NG_032174.1:g.10010T>C
NM_024589.3:c.692T>CMANE SELECT
NP_078865.1:p.Met231Thr
LRG_455:g.10010T>C
NC_000016.9:g.4847942A>G
NR_046480.2:n.699T>C

Protein change:

M231T

Links:

dbSNP: rs1437175362

NCBI 1000 Genomes Browser:

rs1437175362

Molecular consequence:

NM_024589.3:c.692T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_046480.2:n.699T>C - 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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kinesin-like protein KIF27 isoform 1 [Mus musculus]
kinesin-like protein KIF27 isoform 1 [Mus musculus]
gi|32401469|ref|NP_780423.2|

Protein
kinesin-like protein KIF27 [Rattus norvegicus]
kinesin-like protein KIF27 [Rattus norvegicus]
gi|38016129|ref|NP_932167.1|

Protein
ASB3 [Chelonia mydas]
ASB3 [Chelonia mydas]
Gene ID:102947415

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001541532	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 27, 2022)	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

SCV001541532

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 27, 2022)

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, SCV001541532.4

#	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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1043208). 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 replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 231 of the ROGDI protein (p.Met231Thr).

#	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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