NM_024598.4(USB1):c.489_492del (p.Asn163fs) AND Poikiloderma with neutropenia

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Oct 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:: RCV000598593.3

Allele description [Variation Report for NM_024598.4(USB1):c.489_492del (p.Asn163fs)]

NM_024598.4(USB1):c.489_492del (p.Asn163fs)

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.489_492del (p.Asn163fs)

HGVS:

NC_000016.10:g.58014312_58014315del
NG_027698.1:g.17940_17943del
NM_001195302.2:c.450-3022_450-3019del
NM_001330568.2:c.336_339del
NM_024598.4:c.489_492delMANE SELECT
NP_001317497.1:p.Asn112fs
NP_078874.2:p.Asn163fs
NP_078874.2:p.Asn163fs
LRG_352t1:c.489_492del
LRG_352:g.17940_17943del
LRG_352p1:p.Asn163fs
NC_000016.9:g.58048213_58048216del
NC_000016.9:g.58048216_58048219del
NM_024598.3:c.489_492del

Protein change:

N112fs

Links:

OMIM: 613276.0007; dbSNP: rs777667891

NCBI 1000 Genomes Browser:

rs777667891

Molecular consequence:

NM_001330568.2:c.336_339del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024598.4:c.489_492del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001195302.2:c.450-3022_450-3019del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000700250	GeneReviews	no classification provided	not provided	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV001981670	OMIM	no assertion criteria provided	Pathogenic (Oct 20, 2021)	germline	literature only

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000700250

GeneReviews

no classification provided

not provided

germline

literature only

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

SCV001981670

OMIM

no assertion criteria provided

Pathogenic
(Oct 20, 2021)

germline

literature only

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

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

Details of each submission

From GeneReviews, SCV000700250.2

#	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

From OMIM, SCV001981670.1

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

Description

For discussion of the 4-bp deletion (c.489_492del4) in the C16ORF57 gene that was found in compound heterozygous state in a patient with poikiloderma with neutropenia (PN; 604173), see 613276.0005.

#	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: Sep 29, 2024

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