NM_001375380.1(EBF3):c.833dup (p.Ala279fs) AND Hypotonia, ataxia, and delayed development syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 22, 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:: RCV002051909.1

Allele description [Variation Report for NM_001375380.1(EBF3):c.833dup (p.Ala279fs)]

NM_001375380.1(EBF3):c.833dup (p.Ala279fs)

Gene:

EBF3:EBF transcription factor 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

10q26.3

Genomic location:

Preferred name:

NM_001375380.1(EBF3):c.833dup (p.Ala279fs)

HGVS:

NC_000010.11:g.129867866dup
NG_030038.1:g.100967dup
NM_001005463.3:c.806dup
NM_001375379.1:c.833dup
NM_001375380.1:c.833dupMANE SELECT
NM_001375389.1:c.833dup
NM_001375390.1:c.806dup
NM_001375391.1:c.833dup
NM_001375392.1:c.806dup
NP_001005463.1:p.Ala270fs
NP_001362308.1:p.Ala279fs
NP_001362309.1:p.Ala279fs
NP_001362318.1:p.Ala279fs
NP_001362319.1:p.Ala270fs
NP_001362320.1:p.Ala279fs
NP_001362321.1:p.Ala270fs
NC_000010.10:g.131666130dup
NM_001005463.2:c.806dup
NM_001005463.2:c.806dupG

Protein change:

A270fs

Links:

dbSNP: rs1589745620

NCBI 1000 Genomes Browser:

rs1589745620

Molecular consequence:

NM_001005463.3:c.806dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375379.1:c.833dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375380.1:c.833dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375389.1:c.833dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375390.1:c.806dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375391.1:c.833dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001375392.1:c.806dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Hypotonia, ataxia, and delayed development syndrome (HADDS)
Identifiers:: MONDO: MONDO:0015021; MedGen: C4310618; OMIM: 617330

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002318896	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 22, 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

SCV002318896

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 22, 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	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002318896.1

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

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant.It is not observed in the gnomAD v2.1.1 dataset. This variant has been reported as pathogenic (ClinVar ID: VCV000817501, 3billion dataset). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jul 15, 2024

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