NM_001348800.3(ZBTB20):c.1786C>T (p.His596Tyr) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 24, 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:: RCV001861466.4

Allele description [Variation Report for NM_001348800.3(ZBTB20):c.1786C>T (p.His596Tyr)]

NM_001348800.3(ZBTB20):c.1786C>T (p.His596Tyr)

Gene:

ZBTB20:zinc finger and BTB domain containing 20 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q13.31

Genomic location:

Preferred name:

NM_001348800.3(ZBTB20):c.1786C>T (p.His596Tyr)

HGVS:

NC_000003.12:g.114350292G>A
NG_052992.1:g.801989C>T
NM_001164342.2:c.1786C>T
NM_001164343.2:c.1567C>T
NM_001164344.4:c.1567C>T
NM_001164345.4:c.1567C>T
NM_001164346.2:c.1567C>T
NM_001164347.2:c.1567C>T
NM_001348800.3:c.1786C>TMANE SELECT
NM_001348801.3:c.1567C>T
NM_001348802.3:c.1567C>T
NM_001348803.3:c.1786C>T
NM_001348804.3:c.1567C>T
NM_001348805.3:c.1567C>T
NM_001393393.1:c.1786C>T
NM_001393394.1:c.1786C>T
NM_001393395.1:c.1567C>T
NM_001393396.1:c.1567C>T
NM_015642.7:c.1567C>T
NP_001157814.1:p.His596Tyr
NP_001157815.1:p.His523Tyr
NP_001157816.1:p.His523Tyr
NP_001157817.1:p.His523Tyr
NP_001157818.1:p.His523Tyr
NP_001157819.1:p.His523Tyr
NP_001335729.1:p.His596Tyr
NP_001335730.1:p.His523Tyr
NP_001335731.1:p.His523Tyr
NP_001335732.1:p.His596Tyr
NP_001335733.1:p.His523Tyr
NP_001335734.1:p.His523Tyr
NP_001380322.1:p.His596Tyr
NP_001380323.1:p.His596Tyr
NP_001380324.1:p.His523Tyr
NP_001380325.1:p.His523Tyr
NP_056457.3:p.His523Tyr
NC_000003.11:g.114069139G>A
NM_001164342.1:c.1786C>T

Protein change:

H523Y

Links:

dbSNP: rs1057519435

NCBI 1000 Genomes Browser:

rs1057519435

Molecular consequence:

NM_001164342.2:c.1786C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164343.2:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164344.4:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164345.4:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164346.2:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164347.2:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001348800.3:c.1786C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001348801.3:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001348802.3:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001348803.3:c.1786C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001348804.3:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001348805.3:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001393393.1:c.1786C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001393394.1:c.1786C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001393395.1:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001393396.1:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015642.7:c.1567C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002111371	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 24, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25017102, 28327206, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002111371

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 24, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Mutations in ZBTB20 cause Primrose syndrome.

Cordeddu V, Redeker B, Stellacci E, Jongejan A, Fragale A, Bradley TE, Anselmi M, Ciolfi A, Cecchetti S, Muto V, Bernardini L, Azage M, Carvalho DR, Espay AJ, Male A, Molin AM, Posmyk R, Battisti C, Casertano A, Melis D, van Kampen A, Baas F, et al.

Nat Genet. 2014 Aug;46(8):815-7. doi: 10.1038/ng.3035. Epub 2014 Jul 13.

PubMed [citation]

PMID:: 25017102

Lessons learned from additional research analyses of unsolved clinical exome cases.

Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, et al.

Genome Med. 2017 Mar 21;9(1):26. doi: 10.1186/s13073-017-0412-6.

PubMed [citation]

PMID:: 28327206
PMCID:: PMC5361813

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002111371.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.His596 amino acid residue in ZBTB20. Other variant(s) that disrupt this residue have been observed in individuals with ZBTB20-related conditions (PMID: 25017102), which suggests that this may be a clinically significant amino acid residue. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with clinical features of Primrose syndrome (PMID: 28327206). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 375372). This variant is not present in population databases (ExAC no frequency). This sequence change replaces histidine with tyrosine at codon 596 of the ZBTB20 protein (p.His596Tyr). The histidine residue is highly conserved and there is a moderate physicochemical difference between histidine and tyrosine.

#	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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