NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 13, 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:: RCV002074227.20

Allele description [Variation Report for NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly)]

NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly)

Genes:

LOC126806253:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:74057585-74058784 [Gene]
STAMBP:STAM binding protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.1

Genomic location:

Preferred name:

NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly)

HGVS:

NC_000002.12:g.73830968C>G
NG_033223.2:g.7058C>G
NM_001353967.2:c.112C>G
NM_001353968.2:c.112C>G
NM_001353969.2:c.112C>G
NM_001353970.2:c.112C>G
NM_001353971.2:c.-442C>G
NM_001353972.2:c.-203+1972C>G
NM_001353973.2:c.-442C>G
NM_001353974.2:c.-442C>G
NM_001353975.2:c.-442C>G
NM_001353976.2:c.-442C>G
NM_006463.6:c.112C>G
NM_201647.4:c.112C>G
NM_213622.4:c.112C>GMANE SELECT
NP_001340896.1:p.Arg38Gly
NP_001340897.1:p.Arg38Gly
NP_001340898.1:p.Arg38Gly
NP_001340899.1:p.Arg38Gly
NP_006454.1:p.Arg38Gly
NP_964010.1:p.Arg38Gly
NP_998787.1:p.Arg38Gly
NC_000002.11:g.74058095C>G
NR_148668.2:n.160C>G
NR_148669.2:n.160C>G
NR_148670.2:n.340C>G
NR_148671.2:n.674C>G

Protein change:

R38G

Links:

dbSNP: rs143739249

NCBI 1000 Genomes Browser:

rs143739249

Molecular consequence:

NM_001353971.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001353973.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001353974.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001353975.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001353976.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001353972.2:c.-203+1972C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001353967.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353968.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353969.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353970.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006463.6:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_201647.4:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_213622.4:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148668.2:n.160C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148669.2:n.160C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148670.2:n.340C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148671.2:n.674C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002496499	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Feb 1, 2022)	germline	clinical testing	Citation Link,
SCV003338495	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 13, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23542699, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002496499

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Feb 1, 2022)

germline

clinical testing

Citation Link,

SCV003338495

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 13, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	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

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome.

McDonell LM, Mirzaa GM, Alcantara D, Schwartzentruber J, Carter MT, Lee LJ, Clericuzio CL, Graham JM Jr, Morris-Rosendahl DJ, Polster T, Acsadi G, Townshend S, Williams S, Halbert A, Isidor B, David A, Smyser CD, Paciorkowski AR, Willing M, Woulfe J, Das S, Beaulieu CL, et al.

Nat Genet. 2013 May;45(5):556-62. doi: 10.1038/ng.2602. Epub 2013 Mar 31.

PubMed [citation]

PMID:: 23542699
PMCID:: PMC4000253

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 CeGaT Center for Human Genetics Tuebingen, SCV002496499.17

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

#	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		1	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003338495.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 38 of the STAMBP protein (p.Arg38Gly). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with STAMBP-related conditions. ClinVar contains an entry for this variant (Variation ID: 1333643). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant disrupts the p.Arg38 amino acid residue in STAMBP. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 23542699). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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.

#	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

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