NM_006494.4(ERF):c.266A>G (p.Tyr89Cys) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 17, 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:: RCV002518789.2

Allele description [Variation Report for NM_006494.4(ERF):c.266A>G (p.Tyr89Cys)]

NM_006494.4(ERF):c.266A>G (p.Tyr89Cys)

Gene:

ERF:ETS2 repressor factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.2

Genomic location:

Preferred name:

NM_006494.4(ERF):c.266A>G (p.Tyr89Cys)

HGVS:

NC_000019.10:g.42249934T>C
NG_042802.1:g.10231A>G
NM_001301035.2:c.41A>G
NM_001308402.2:c.41A>G
NM_001312656.2:c.41A>G
NM_006494.4:c.266A>GMANE SELECT
NP_001287964.1:p.Tyr14Cys
NP_001295331.1:p.Tyr14Cys
NP_001299585.1:p.Tyr14Cys
NP_006485.2:p.Tyr89Cys
NC_000019.9:g.42754086T>C
NM_006494.2:c.266A>G

Protein change:

Y14C; TYR89CYS

Links:

OMIM: 611888.0008; dbSNP: rs886041001

NCBI 1000 Genomes Browser:

rs886041001

Molecular consequence:

NM_001301035.2:c.41A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001308402.2:c.41A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001312656.2:c.41A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006494.4:c.266A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003564122	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Dec 17, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 27738187, 30569521, 30728880, 32592542 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003564122

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Dec 17, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

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

Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene.

Balasubramanian M, Lord H, Levesque S, Guturu H, Thuriot F, Sillon G, Wenger AM, Sureka DL, Lester T, Johnson DS, Bowen J, Calhoun AR, Viskochil DH; DDD Study., Bejerano G, Bernstein JA, Chitayat D.

J Med Genet. 2017 Mar;54(3):157-165. doi: 10.1136/jmedgenet-2016-104143. Epub 2016 Oct 13.

PubMed [citation]

PMID:: 27738187

Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p.(Tyr89Cys) pathogenic variant in the ERF gene.

Caro-Contreras A, Alcántara-Ortigoza MA, Ahumada-Pérez JF, González-Del Angel A.

Am J Med Genet A. 2019 Jan;179(1):118-122. doi: 10.1002/ajmg.a.60676. Epub 2018 Dec 20.

PubMed [citation]

PMID:: 30569521

See all PubMed Citations (4)

Details of each submission

From Ambry Genetics, SCV003564122.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

The c.266A>G (p.Y89C) alteration is located in exon 3 (coding exon 3) of the ERF gene. This alteration results from a A to G substitution at nucleotide position 266, causing the tyrosine (Y) at amino acid position 89 to be replaced by a cysteine (C). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration is a recurrent alteration reported in multiple unrelated individuals with Chitayat syndrome. This alteration occurred de novo in at least three separate patients and was inherited from an affected parent in two families (Balasubramanian, 2016; Caro-Contreras, 2019; Shin, 2019; Suter, 2020; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

#	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: Jun 23, 2024

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