NM_005861.4(STUB1):c.829C>T (p.Gln277Ter) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jul 23, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV002244433.6

Allele description [Variation Report for NM_005861.4(STUB1):c.829C>T (p.Gln277Ter)]

NM_005861.4(STUB1):c.829C>T (p.Gln277Ter)

Genes:

STUB1:STIP1 homology and U-box containing protein 1 [Gene - OMIM - HGNC]
JMJD8:jumonji domain containing 8 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_005861.4(STUB1):c.829C>T (p.Gln277Ter)

HGVS:

NC_000016.10:g.682406C>T
NG_034141.1:g.7296C>T
NG_132623.1:g.730C>T
NM_001005920.4:c.*388G>AMANE SELECT
NM_001293197.2:c.613C>T
NM_001323918.3:c.*422G>A
NM_001323919.3:c.*388G>A
NM_001323920.3:c.*388G>A
NM_001323922.3:c.*422G>A
NM_005861.4:c.829C>TMANE SELECT
NP_001280126.1:p.Gln205Ter
NP_005852.2:p.Gln277Ter
NC_000016.9:g.732406C>T
NM_005861.2:c.829C>T
NR_136650.3:n.1281G>A
NR_136651.3:n.1286G>A
NR_136652.3:n.1196G>A

Protein change:

Q205*

Links:

dbSNP: rs2151507113

NCBI 1000 Genomes Browser:

rs2151507113

Molecular consequence:

NM_001005920.4:c.*388G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001323918.3:c.*422G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001323919.3:c.*388G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001323920.3:c.*388G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001323922.3:c.*422G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NR_136650.3:n.1281G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136651.3:n.1286G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136652.3:n.1196G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001293197.2:c.613C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005861.4:c.829C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

tq88a11.x1 NCI_CGAP_Ov23 Homo sapiens cDNA clone IMAGE:2215868 3', mRNA sequence
tq88a11.x1 NCI_CGAP_Ov23 Homo sapiens cDNA clone IMAGE:2215868 3', mRNA sequence
gi|4525692|gnl|dbEST|2383439|gb|AI5 .1|

Nucleotide
RecName: Full=Large ribosomal subunit protein uL22c; AltName: Full=50S ribosomal...
RecName: Full=Large ribosomal subunit protein uL22c; AltName: Full=50S ribosomal protein L22, chloroplastic
gi|109893080|sp|Q2MIE8.1|RK22_SOLBU

Protein
RecName: Full=Putative disease resistance protein RGA4; AltName: Full=RGA4-blb
RecName: Full=Putative disease resistance protein RGA4; AltName: Full=RGA4-blb
gi|46576965|sp|Q7XA39.1|RGA4_SOLBU

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002513073	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jul 23, 2024)	germline	clinical testing	Citation Link,
SCV003219933	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 12, 2022)	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

SCV002513073

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jul 23, 2024)

germline

clinical testing

Citation Link,

SCV003219933

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 12, 2022)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 GeneDx, SCV002513073.3

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation, as the last 27 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003219933.2

#	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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 1683911). This variant has not been reported in the literature in individuals affected with STUB1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln277*) in the STUB1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 27 amino acid(s) of the STUB1 protein.

#	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: Oct 8, 2024

ClinVar

Relating variation to medicine