NC_000002.11:g.(?_71004499)_(74779761_?)del AND not provided

Germline classification:: no classifications from unflagged records (1 submission)
Review status:: no classifications from unflagged records

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:: RCV003107716.6

Allele description [Variation Report for NC_000002.11:g.(?_71004499)_(74779761_?)del]

NC_000002.11:g.(?_71004499)_(74779761_?)del

Genes:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]
ATP6V1B1:ATPase H+ transporting V1 subunit B1 [Gene - OMIM - HGNC]
AUP1:AUP1 lipid droplet regulating VLDL assembly factor [Gene - OMIM - HGNC]
CLEC4F:C-type lectin domain family 4 member F [Gene - OMIM - HGNC]
CD207:CD207 molecule [Gene - OMIM - HGNC]
DQX1:DEAQ-box RNA dependent ATPase 1 [Gene - OMIM - HGNC]
FBXO41:F-box protein 41 [Gene - OMIM - HGNC]
HTRA2:HtrA serine peptidase 2 [Gene - OMIM - HGNC]
INO80B:INO80 complex subunit B [Gene - OMIM - HGNC]
MPHOSPH10:M-phase phosphoprotein 10 [Gene - OMIM - HGNC]
MOB1A:MOB kinase activator 1A [Gene - OMIM - HGNC]
NAGK:N-acetylglucosamine kinase [Gene - OMIM - HGNC]
NAT8:N-acetyltransferase 8 (putative) [Gene - OMIM - HGNC]
NAT8B:N-acetyltransferase 8B (putative, gene/pseudogene) [Gene - OMIM - HGNC]
RAB11FIP5:RAB11 family interacting protein 5 [Gene - OMIM - HGNC]
SMYD5:SMYD family member 5 [Gene - OMIM - HGNC]
STAMBP:STAM binding protein [Gene - OMIM - HGNC]
TLX2:T cell leukemia homeobox 2 [Gene - OMIM - HGNC]
TPRKB:TP53RK binding protein [Gene - OMIM - HGNC]
WDR54:WD repeat domain 54 [Gene - OMIM - HGNC]
WBP1:WW domain binding protein 1 [Gene - OMIM - HGNC]
ACTG2:actin gamma 2, smooth muscle [Gene - OMIM - HGNC]
ANKRD53:ankyrin repeat domain 53 [Gene - OMIM - HGNC]
BOLA3:bolA family member 3 [Gene - OMIM - HGNC]
CCT7:chaperonin containing TCP1 subunit 7 [Gene - OMIM - HGNC]
C2orf78:chromosome 2 open reading frame 78 [Gene - HGNC]
C2orf81:chromosome 2 open reading frame 81 [Gene - HGNC]
CCDC142:coiled-coil domain containing 142 [Gene - HGNC]
CYP26B1:cytochrome P450 family 26 subfamily B member 1 [Gene - OMIM - HGNC]
DGUOK:deoxyguanosine kinase [Gene - OMIM - HGNC]
DOK1:docking protein 1 [Gene - OMIM - HGNC]
DUSP11:dual specificity phosphatase 11 [Gene - OMIM - HGNC]
DCTN1:dynactin subunit 1 [Gene - OMIM - HGNC]
DYSF:dysferlin [Gene - OMIM - HGNC]
EGR4:early growth response 4 [Gene - OMIM - HGNC]
EMX1:empty spiracles homeobox 1 [Gene - OMIM - HGNC]
EXOC6B:exocyst complex component 6B [Gene - OMIM - HGNC]
FIGLA:folliculogenesis specific bHLH transcription factor [Gene - OMIM - HGNC]
LBX2:ladybird homeobox 2 [Gene - OMIM - HGNC]
LOXL3:lysyl oxidase like 3 [Gene - OMIM - HGNC]
MOGS:mannosyl-oligosaccharide glucosidase [Gene - OMIM - HGNC]
MTHFD2:methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Gene - OMIM - HGNC]
MCEE:methylmalonyl-CoA epimerase [Gene - OMIM - HGNC]
MRPL53:mitochondrial ribosomal protein L53 [Gene - OMIM - HGNC]
NOTO:notochord homeobox [Gene - OMIM - HGNC]
PAIP2B:poly(A) binding protein interacting protein 2B [Gene - OMIM - HGNC]
PCGF1:polycomb group ring finger 1 [Gene - OMIM - HGNC]
PRADC1:protease associated domain containing 1 [Gene - OMIM - HGNC]
RTKN:rhotekin [Gene - OMIM - HGNC]
SPR:sepiapterin reductase [Gene - OMIM - HGNC]
SFXN5:sideroflexin 5 [Gene - OMIM - HGNC]
SLC4A5:solute carrier family 4 member 5 [Gene - OMIM - HGNC]
TEX261:testis expressed 261 [Gene - OMIM - HGNC]
TET3:tet methylcytosine dioxygenase 3 [Gene - OMIM - HGNC]
TTC31:tetratricopeptide repeat domain 31 [Gene - HGNC]
VAX2:ventral anterior homeobox 2 [Gene - OMIM - HGNC]
ZNF638:zinc finger protein 638 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p13.3-13.1

Genomic location:

Chr2: 71004499 - 74779761 (on Assembly GRCh37)

Preferred name:

NC_000002.11:g.(?_71004499)_(74779761_?)del

HGVS:

NC_000002.11:g.(?_71004499)_(74779761_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

No clinical assertions found. See "Flagged submissions" below.

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003791500.2

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the STAMBP gene has been identified. Loss-of-function variants in STAMBP are known to be pathogenic (PMID: 23542699). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with STAMBP-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791500	Labcorp Genetics (formerly Invitae), Labcorp	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV003791500 appears to be redundant with SCV003795744. (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 8, 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

SCV003791500

Labcorp Genetics (formerly Invitae), Labcorp

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV003791500 appears to be redundant with SCV003795744.

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 8, 2022)

germline

clinical testing

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine