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NM_014797.3(ZBTB24):c.1753A>T (p.Thr585Ser) AND Immunodeficiency-centromeric instability-facial anomalies syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 24, 2019
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:
RCV001205565.6

Allele description

NM_014797.3(ZBTB24):c.1753A>T (p.Thr585Ser)

Gene:
ZBTB24:zinc finger and BTB domain containing 24 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q21
Genomic location:
Preferred name:
NM_014797.3(ZBTB24):c.1753A>T (p.Thr585Ser)
HGVS:
  • NC_000006.12:g.109466192T>A
  • NG_029388.1:g.22046A>T
  • NG_042833.1:g.4777A>T
  • NM_014797.3:c.1753A>TMANE SELECT
  • NP_055612.2:p.Thr585Ser
  • LRG_326t1:c.1753A>T
  • LRG_326:g.22046A>T
  • NC_000006.11:g.109787395T>A
  • NM_014797.2:c.1753A>T
Protein change:
T585S
Links:
dbSNP: rs1776035641
NCBI 1000 Genomes Browser:
rs1776035641
Molecular consequence:
  • NM_014797.3:c.1753A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Immunodeficiency-centromeric instability-facial anomalies syndrome 2 (ICF2)
Identifiers:
MONDO: MONDO:0013553; MedGen: C3279748; Orphanet: 2268; OMIM: 614069

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001376827Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 24, 2019) 		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 Invitae, SCV001376827.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with ZBTB24-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with serine at codon 585 of the ZBTB24 protein (p.Thr585Ser). The threonine residue is moderately conserved and there is a small physicochemical difference between threonine and serine.

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

Last Updated: Feb 28, 2024