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Primary immunodeficiency

Gene: NOP10

Amber List (moderate evidence)

NOP10 (NOP10 ribonucleoprotein)
EnsemblGeneIds (GRCh38): ENSG00000182117
EnsemblGeneIds (GRCh37): ENSG00000182117
OMIM: 606471, Gene2Phenotype
NOP10 is in 14 panels

4 reviews

Zornitza Stark (Australian Genomics)

Red List (low evidence)

Single family reported.
Created: 11 Apr 2020, 4:46 a.m. | Last Modified: 11 Apr 2020, 4:46 a.m.
Panel Version: 2.51

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Dyskeratosis congenita, autosomal recessive 1, MIM#224230

Publications

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 1 variant reported in 3 affected members of a consanguineous Saudi Arabian family.
Created: 9 May 2018, 8:56 a.m.

Louise Daugherty (Genomics England Curator)

I don't know

One family reported, therefore left Amber until further evidence to support Green rating by external expert
Created: 11 Jul 2018, 4:13 p.m.
One family with a homozygous NOP10 pathogenic variant, c.100C>T (p.Arg34Trp), in the affected individual has been described Walne et al. 2007 (PMID: 17507419). The reported pathogenic variant resulted in reduced TERC levels and shortened telomeres.
Created: 4 Jul 2018, 4:45 p.m.
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): NOP10 .PanelApp HGNC gene symbol check: NOP10 . IUIS Disease: AR-DKC due to nucleolar protein family A member 3 (NHP3) or NOP10 deficiency . IUIS Inheritance: AR .T cells: Normal, .B cells: Variable, .IUIS Other affected cells: N/A. IUIS Associated features: Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: DyskeratosIs Congenita (DKC), Myelodysplasia, Short Telomeres
Created: 2 Jul 2018, 10:35 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s) GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 20 Apr 2018, 12:25 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: NOP10, PanelApp HGNC gene symbol check: NOP10, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / Dyskeratosis congenita / Dyskeratosis congenita; Other well defined PIDs / Dyskeratosis congenita / Hoyeraal-Hreidarsson syndrome
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: NOP10, GRID_Gene_Symbol: NOP10, GRID_Transcript_ENS_Community submitted: ENST00000328848, GRID_Transcript_RefSeq: NM_018648.3, GRID_Transcript_ENS_used_on_Production: ENST00000328848
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Dyskeratosis congenita, autosomal recessive 1 224230
  • Dyskeratosis congenita 1
  • Dyskeratosis congenita
  • Hoyeraal-Hreidarsson syndrome
  • Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients
  • Combined immunodeficiencies with associated or syndromic features
OMIM
606471
Clinvar variants
Variants in NOP10
Penetrance
None
Publications
Panels with this gene

History Filter Activity

12 Jul 2018, Gel status: 2

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

11 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: nop10 has been classified as Amber List (Moderate Evidence).

1 Jul 2018, Gel status: 2

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene NOP10 were set to Dyskeratosis congenita, autosomal recessive 1 224230, Dyskeratosis congenita 1, Dyskeratosis congenita, Hoyeraal-Hreidarsson syndrome, Intrauterine growth retardation, microcephaly, nail dystrophy, sparse scalp hair and eyelashes, hyperpigmentation of skin, palmar hyperkeratosis, premalignant oral leukoplakia, pancytopenia, myelodysplasia, +/- recurrent infections. A severe phenotype with developmental delay and cerebellar hypoplasia known as Hoyeraal-Hreidarsson Syndrome (HHS) may occur in some DKC patients, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to NOP10. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to NOP10. Panel: Primary immunodeficiency disorders

9 May 2018, Gel status: 2

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

9 May 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for NOP10 were set to 17507419

9 May 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for NOP10 were set to Dyskeratosis congenita, autosomal recessive 1 224230; Dyskeratosis congenita 1; Dyskeratosis congenita; Hoyeraal-Hreidarsson syndrome

20 Apr 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Expert Review Amber was added to NOP10. Panel: Primary immunodeficiency disorders

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to NOP10. Panel: Primary immunodeficiency disorders Phenotypes for gene NOP10 were set to Dyskeratosis congenita 1, Dyskeratosis congenita, Hoyeraal-Hreidarsson syndrome

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene NOP10 were set to Dyskeratosis congenita 1

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

NOP10 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

NOP10 was created by Louise Daugherty