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NM_148919.4(PSMB8):c.224C>T (p.Thr75Met) AND Proteasome-associated autoinflammatory syndrome 1

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Sep 1, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000816894.5

Allele description [Variation Report for NM_148919.4(PSMB8):c.224C>T (p.Thr75Met)]

NM_148919.4(PSMB8):c.224C>T (p.Thr75Met)

Gene:
PSMB8:proteasome 20S subunit beta 8 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.32
Genomic location:
Preferred name:
NM_148919.4(PSMB8):c.224C>T (p.Thr75Met)
HGVS:
  • NC_000006.12:g.32843013G>A
  • NG_009793.3:g.758C>T
  • NG_028165.1:g.6923C>T
  • NM_004159.5:c.212C>T
  • NM_148919.4:c.224C>TMANE SELECT
  • NP_004150.1:p.Thr71Met
  • NP_683720.2:p.Thr75Met
  • LRG_1328t1:c.224C>T
  • LRG_1328t2:c.212C>T
  • LRG_1328:g.6923C>T
  • LRG_1328p1:p.Thr75Met
  • LRG_1328p2:p.Thr71Met
  • NC_000006.11:g.32810790G>A
  • NM_148919.3:c.224C>T
Note:
ClinGen staff contributed the HGVS expression for this variant.
Protein change:
T71M; THR75MET
Links:
OMIM: 177046.0001; dbSNP: rs748082671
NCBI 1000 Genomes Browser:
rs748082671
Molecular consequence:
  • NM_004159.5:c.212C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_148919.4:c.224C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Proteasome-associated autoinflammatory syndrome 1 (PRAAS1)
Synonyms:
Nakajo syndrome; Nodular erythema digital changes; JOINT CONTRACTURES, MUSCULAR ATROPHY, MICROCYTIC ANEMIA, AND PANNICULITIS-INDUCED LIPODYSTROPHY; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0054698; MedGen: C4746851; Orphanet: 2615; Orphanet: 324977; Orphanet: 324999; Orphanet: 325004; OMIM: 256040

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000044027OMIM
no assertion criteria provided
Pathogenic
(Mar 1, 2012)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV002599017Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Sep 1, 2022)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE) syndrome.

Torrelo A, Patel S, Colmenero I, Gurbindo D, Lendínez F, Hernández A, López-Robledillo JC, Dadban A, Requena L, Paller AS.

J Am Acad Dermatol. 2010 Mar;62(3):489-95. doi: 10.1016/j.jaad.2009.04.046.

PubMed [citation]
PMID:
20159315

An autosomal recessive syndrome of joint contractures, muscular atrophy, microcytic anemia, and panniculitis-associated lipodystrophy.

Garg A, Hernandez MD, Sousa AB, Subramanyam L, Martínez de Villarreal L, dos Santos HG, Barboza O.

J Clin Endocrinol Metab. 2010 Sep;95(9):E58-63. doi: 10.1210/jc.2010-0488. Epub 2010 Jun 9.

PubMed [citation]
PMID:
20534754
PMCID:
PMC2936059
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000044027.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)

Description

In 3 affected members from 2 unrelated families with proteasome-associated autoinflammatory syndrome-1 (PRAAS1; 256040), Agarwal et al. (2010) identified a homozygous 224C-T transition in exon 2 of the PSMB8 gene, resulting in a thr75-to-met (T75M) substitution in a highly conserved residue. The mutation was not found in 275 controls but was present in heterozygosity in available parents and unaffected sibs. The patients had previously been reported by Garg et al. (2010) and were of Portuguese and Mexican origin, respectively. The parents of the Portuguese patients were consanguineous, whereas consanguinity was suspected in the parents of the Mexican patients. Haplotype analysis indicated identity by descent, but the mutation appeared to be ancient. Molecular dynamics simulation indicated that the mutation relaxed the protein structure by 1.2 angstrom, and may affect the proteolytic processing of peptides. Studies of patient lymphocytes showed that the mutant protein had markedly decreased chymotrypsin-like activity compared to wildtype, consistent with a decrease in proteasomal activity and loss of function. Laboratory studies of the 2 Mexican sibs performed by Agarwal et al. (2010) showed that both had significantly increased levels of serum IL6 (147620) and gamma-interferon (IFNG; 147570), and 1 had increased IL8 (146930). Other cytokines were not elevated, suggesting a particular biomarker signature. The disorder is characterized by childhood onset of joint stiffness and severe contractures of the hands and feet, erythematous skin lesions with subsequent development of severe lipodystrophy, and laboratory evidence of immune dysregulation. Accompanying features include muscle weakness and atrophy, hepatosplenomegaly, and microcytic anemia. The findings indicated that dysfunction of the immunoproteasome can result in an autoinflammatory disease.

Liu et al. (2012) identified a homozygous T75M mutation in 4 unrelated patients (patients 1, 2, 5, and 8) with PRAAS1. The deceased sister of patient 2 (patient 3) was similarly affected and assumed to carry the same homozygous mutation. Patients 1, 2, 3, and 4 had previously been reported by Torrelo et al. (2010). The clinical features were similar to those reported by Garg et al. (2010). Patients 3, 4, and 8 reported by Liu et al. (2012) were of Hispanic origin and patients 1 and 2 were of Spanish origin. However, only 2 patients shared the same haplotype, suggesting that T75 is a mutational hotspot. Two additional patients (patients 7 and 9) reported by Liu et al. (2012) were heterozygous for the T75M mutation, but a second mutation was not detected.

In the 2 patients (patients 7 and 9) with PRAAS1 reported by Liu et al. (2012) who were heterozygous for the T75M mutation, Brehm et al. (2015) identified heterozygous mutations in the PSMA3 gene (176843.0001 and 176843.0002) on the other allele, indicating digenic inheritance. Brehm et al. (2015) referred to the patients as patient 2 (American/Caucasian origin) and patient 3 (Spanish origin).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002599017.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: PSMB8 c.224C>T (p.Thr75Met) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 246860 control chromosomes. c.224C>T has been reported in the literature as a homozygous genotype in multiple individuals with features of immune-dysregulatory disease chronic atypical neutrophilic dermatosis with lipodystrophy (example, Agarwal_2010) and elevated temperature (CANDLE), which is classified as a proteasome-associated autoinflammatory syndrome (PRAAS) (example, Liu_2012). It has also been reported in a model of digenic inheritance with double heterozygosity for this variant (in a gene encoding an inducible proteasome subunit) along with another mutation in a gene encoding a constitutive proteasome subunit (PSMA3 gene) (example, Brehm_2015) in at-least two individuals with features of PRAAS syndrome. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in significantly reduced chymotrypsin-like proteolytic activity (approximately 30% of wild-type) mediated by immunoproteasomes (example, Agarwal_2010). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024