NM_002128.7(HMGB1):c.47_48del (p.Tyr16fs) AND HMGB1-associated disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 27, 2023
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:: RCV003448547.1

Allele description [Variation Report for NM_002128.7(HMGB1):c.47_48del (p.Tyr16fs)]

NM_002128.7(HMGB1):c.47_48del (p.Tyr16fs)

Gene:

HMGB1:high mobility group box 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

13q12.3

Genomic location:

Preferred name:

NM_002128.7(HMGB1):c.47_48del (p.Tyr16fs)

HGVS:

NC_000013.11:g.30463633AT[1]
NM_001313892.2:c.47_48del
NM_001313893.1:c.47_48del
NM_001363661.2:c.47_48del
NM_001370339.1:c.47_48del
NM_001370340.1:c.47_48del
NM_001370341.1:c.47_48del
NM_002128.7:c.47_48delMANE SELECT
NP_001300821.1:p.Tyr16fs
NP_001300822.1:p.Tyr16fs
NP_001350590.1:p.Tyr16fs
NP_001357268.1:p.Tyr16fs
NP_001357269.1:p.Tyr16fs
NP_001357270.1:p.Tyr16fs
NP_002119.1:p.Tyr16fs
NC_000013.10:g.31037770AT[1]

Protein change:

Y16fs

Molecular consequence:

NM_001313892.2:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001313893.1:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001363661.2:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370339.1:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370340.1:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370341.1:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002128.7:c.47_48del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: HMGB1-associated disorder
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176002	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 27, 2023)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34164801, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004176002

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 27, 2023)

de novo

clinical testing

PubMed (2)
[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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Heterozygous HMGB1 loss-of-function variants are associated with developmental delay and microcephaly.

Uguen K, Krysiak K, Audebert-Bellanger S, Redon S, Benech C, Viora-Dupont E, Tran Mau-Them F, Rondeau S, Elsharkawi I, Granadillo JL, Neidich J, Soares CA, Tkachenko N, M Amudhavalli S, Engleman K, Boland A, Deleuze JF, Bezieau S, Odent S, Toutain A, Bonneau D, Gilbert-Dussardier B, et al.

Clin Genet. 2021 Oct;100(4):386-395. doi: 10.1111/cge.14015. Epub 2021 Jun 28.

PubMed [citation]

PMID:: 34164801

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 Institute of Human Genetics, University of Leipzig Medical Center, SCV004176002.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Criteria applied: PVS1_STR,PS2_MOD,PM2_SUP

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

Last Updated: Dec 24, 2023

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