NM_024598.4(USB1):c.504-2A>C AND Poikiloderma with neutropenia

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 1, 2010
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:: RCV000000224.6

Allele description [Variation Report for NM_024598.4(USB1):c.504-2A>C]

NM_024598.4(USB1):c.504-2A>C

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

16q21

Genomic location:

Preferred name:

NM_024598.4(USB1):c.504-2A>C

HGVS:

NC_000016.10:g.58017332A>C
NG_027698.1:g.20960A>C
NM_001195302.2:c.450-2A>C
NM_001330568.2:c.351-2A>C
NM_024598.4:c.504-2A>CMANE SELECT
LRG_352t1:c.504-2A>C
LRG_352:g.20960A>C
NC_000016.9:g.58051236A>C
NM_024598.3:c.504-2A>C

Nucleotide change:

IVS4AS, A-C, -1

Links:

OMIM: 613276.0001; dbSNP: rs137853970

NCBI 1000 Genomes Browser:

rs137853970

Molecular consequence:

NM_001195302.2:c.450-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001330568.2:c.351-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_024598.4:c.504-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV000020368	OMIM	no assertion criteria provided	Pathogenic (Jan 1, 2010)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000700232	GeneReviews	no classification provided	not provided	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

SCV000020368

OMIM

no assertion criteria provided

Pathogenic
(Jan 1, 2010)

germline

literature only

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

SCV000700232

GeneReviews

no classification provided

not provided

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

Citations

PubMed

Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene.

Volpi L, Roversi G, Colombo EA, Leijsten N, Concolino D, Calabria A, Mencarelli MA, Fimiani M, Macciardi F, Pfundt R, Schoenmakers EF, Larizza L.

Am J Hum Genet. 2010 Jan;86(1):72-6. doi: 10.1016/j.ajhg.2009.11.014. Epub 2009 Dec 10. Erratum in: Am J Hum Genet. 2010 Sep 10;87(3):445.

PubMed [citation]

PMID:: 20004881
PMCID:: PMC2801743

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, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 29072891

Details of each submission

From OMIM, SCV000020368.3

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

Description

In 3 affected sibs from a highly consanguineous Italian family with poikiloderma and neutropenia (PN; 604173), Volpi et al. (2010) identified homozygosity for a 504-2A-C transversion at the splice acceptor site in intron 4 of the C16ORF57 gene. Subsequent cDNA analysis in an affected sib revealed an aberrant transcript that was 106 nucleotides shorter than normal due to skipping of exon 5.

#	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

From GeneReviews, SCV000700232.2

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

#	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 10, 2023

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