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NM_014797.3(ZBTB24):c.2041C>T (p.Pro681Ser) AND Immunodeficiency-centromeric instability-facial anomalies syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 19, 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:
RCV003093249.8

Allele description

NM_014797.3(ZBTB24):c.2041C>T (p.Pro681Ser)

Genes:
MICAL1:microtubule associated monooxygenase, calponin and LIM domain containing 1 [Gene - OMIM - HGNC]
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.2041C>T (p.Pro681Ser)
HGVS:
  • NC_000006.12:g.109465904G>A
  • NG_029388.1:g.22334C>T
  • NG_042833.1:g.5065C>T
  • NM_001286613.2:c.-227C>T
  • NM_014797.3:c.2041C>TMANE SELECT
  • NP_055612.2:p.Pro681Ser
  • NP_055612.2:p.Pro681Ser
  • LRG_326t1:c.2041C>T
  • LRG_326:g.22334C>T
  • LRG_326p1:p.Pro681Ser
  • NC_000006.11:g.109787107G>A
  • NM_014797.2:c.2041C>T
Protein change:
P681S
Molecular consequence:
  • NM_001286613.2:c.-227C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_014797.3:c.2041C>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
SCV003483559Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 19, 2022) 		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, SCV003483559.1

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

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 681 of the ZBTB24 protein (p.Pro681Ser). This variant is present in population databases (rs775492598, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with ZBTB24-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

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

Last Updated: Sep 16, 2024