NM_148919.4(PSMB8):c.170T>C (p.Leu57Pro) AND Proteosome-associated autoinflammatory syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 26, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003761198.3

Allele description [Variation Report for NM_148919.4(PSMB8):c.170T>C (p.Leu57Pro)]

NM_148919.4(PSMB8):c.170T>C (p.Leu57Pro)

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.170T>C (p.Leu57Pro)

HGVS:

NC_000006.12:g.32843067A>G
NG_009793.4:g.704T>C
NG_028165.1:g.6869T>C
NM_004159.5:c.158T>C
NM_148919.4:c.170T>CMANE SELECT
NP_004150.1:p.Leu53Pro
NP_683720.2:p.Leu57Pro
LRG_1328t1:c.170T>C
LRG_1328t2:c.158T>C
LRG_1328:g.6869T>C
LRG_1328p1:p.Leu57Pro
LRG_1328p2:p.Leu53Pro
LRG_167:g.704T>C
NC_000006.11:g.32810844A>G
NG_009793.3:g.704T>C

Protein change:

L53P

Links:

dbSNP: rs1770032427

NCBI 1000 Genomes Browser:

rs1770032427

Molecular consequence:

NM_004159.5:c.158T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_148919.4:c.170T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Proteosome-associated autoinflammatory syndrome
Synonyms:: Proteasome-associated autoinflammatory syndrome
Identifiers:: MONDO: MONDO:0009726; MedGen: C1850568; OMIM: PS256040

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JGI_XZG64922.fwd NIH_XGC_tropGas7 Xenopus tropicalis cDNA clone IMAGE:7578945 5'...
JGI_XZG64922.fwd NIH_XGC_tropGas7 Xenopus tropicalis cDNA clone IMAGE:7578945 5', mRNA sequence
gi|74266030|gnl|dbEST|31352085|gb|C 72.2|

Nucleotide
Stevenson-Carey syndrome
Stevenson-Carey syndrome

MedGen
Hypoplastic philtrum
Hypoplastic philtrum

MedGen
SACOL1334 AND (alive[prop]) (0)
Gene
SAV0883 AND (alive[prop]) (0)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001546903	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 26, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001546903

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 26, 2023)

germline

clinical testing

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	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001546903.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬† is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1047618). This variant has not been reported in the literature in individuals affected with PSMB8-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 57 of the PSMB8 protein (p.Leu57Pro).

#	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: Nov 3, 2024

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