NM_024598.4(USB1):c.531del (p.His179fs) AND Poikiloderma with neutropenia

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Dec 20, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000598696.3

Allele description [Variation Report for NM_024598.4(USB1):c.531del (p.His179fs)]

NM_024598.4(USB1):c.531del (p.His179fs)

Gene:

USB1:U6 snRNA biogenesis phosphodiesterase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q21

Genomic location:

Preferred name:

NM_024598.4(USB1):c.531del (p.His179fs)

HGVS:

NC_000016.10:g.58017361del
NG_027698.1:g.20989del
NM_001195302.2:c.477del
NM_001330568.2:c.378del
NM_024598.4:c.531delMANE SELECT
NP_001182231.1:p.His161fs
NP_001317497.1:p.His128fs
NP_078874.2:p.His179fs
LRG_352:g.20989del
NC_000016.9:g.58051265del
NM_024598.2:c.531delA
NM_024598.3:c.531delA
NP_078874.2:p.(His179MetfsTer86)

Protein change:

H128fs

Links:

OMIM: 613276.0010; dbSNP: rs1555498565

NCBI 1000 Genomes Browser:

rs1555498565

Molecular consequence:

NM_001195302.2:c.477del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330568.2:c.378del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024598.4:c.531del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Poikiloderma with neutropenia (PN)
Synonyms:: Poikiloderma with neutropenia Clericuzio type
Identifiers:: MONDO: MONDO:0011405; MedGen: C1858723; Orphanet: 221046; OMIM: 604173

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000700233	GeneReviews	no classification provided	not provided	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002039155	OMIM	no assertion criteria provided	Pathogenic (Dec 20, 2021)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000700233

GeneReviews

no classification provided

not provided

germline

literature only

PubMed (1)
[See all records that cite this PMID]

SCV002039155

OMIM

no assertion criteria provided

Pathogenic
(Dec 20, 2021)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Poikiloderma with Neutropenia.

Wang L, Clericuzio C, Larizza L, Concolino D.

2017 Oct 26 [updated 2024 Feb 22]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 29072891

Insights into Mutation Effect in Three Poikiloderma with Neutropenia Patients by Transcript Analysis and Disease Evolution of Reported Patients with the Same Pathogenic Variants.

Colombo EA, Elcioglu NH, Graziano C, Farinelli P, Di Fede E, Neri I, Facchini E, Greco M, Gervasini C, Larizza L.

J Clin Immunol. 2018 May;38(4):494-502. doi: 10.1007/s10875-018-0508-9. Epub 2018 May 16.

PubMed [citation]

PMID:: 29770900

Details of each submission

From GeneReviews, SCV000700233.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

c.531delA was identified in 12 unrelated Turkish families

#	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

From OMIM, SCV002039155.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a Turkish boy (patient 32) with poikiloderma with neutropenia (PN; 604173), Colombo et al. (2018) identified homozygosity for a 1-bp deletion (c.531delA, NM_024598.2) in exon 5 of the USB1 gene, predicted to result in a frameshift (His179fsTer86) with the same amino acid length as the wildtype protein but with a different composition of the last 85 residues at the C terminus. The mutation was identified by USB1 gene sequencing, and the parents were shown to be mutation carriers. The mutation was predicted to lead to loss of a tetrapeptide motif and affect the 2H active site.

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

Last Updated: Oct 1, 2022

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