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NC_000007.13:g.(?_98983338)_(100860555_?)del AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 5, 2022
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:
RCV001877526.5

Allele description

NC_000007.13:g.(?_98983338)_(100860555_?)del

Genes:
  • ATP5MF:ATP synthase membrane subunit f [Gene - OMIM - HGNC]
  • ATP5MF-PTCD1:ATP5MF-PTCD1 readthrough [Gene - HGNC]
  • AGFG2:ArfGAP with FG repeats 2 [Gene - OMIM - HGNC]
  • BUD31:BUD31 homolog [Gene - OMIM - HGNC]
  • COPS6:COP9 signalosome subunit 6 [Gene - OMIM - HGNC]
  • EPHB4:EPH receptor B4 [Gene - OMIM - HGNC]
  • FBXO24:F-box protein 24 [Gene - OMIM - HGNC]
  • GNB2:G protein subunit beta 2 [Gene - OMIM - HGNC]
  • GIGYF1:GRB10 interacting GYF protein 1 [Gene - OMIM - HGNC]
  • NAT16:N-acetyltransferase 16 (putative) [Gene - OMIM - HGNC]
  • PDAP1:PDGFA associated protein 1 [Gene - OMIM - HGNC]
  • POP7:POP7 homolog, ribonuclease P/MRP subunit [Gene - OMIM - HGNC]
  • PVRIG:PVR related immunoglobulin domain containing [Gene - OMIM - HGNC]
  • STAG3:STAG3 cohesin complex component [Gene - OMIM - HGNC]
  • SAP25:Sin3A associated protein 25 [Gene - OMIM - HGNC]
  • TAF6:TATA-box binding protein associated factor 6 [Gene - OMIM - HGNC]
  • TSC22D4:TSC22 domain family member 4 [Gene - OMIM - HGNC]
  • UFSP1:UFM1 specific peptidase 1 (inactive) [Gene - OMIM - HGNC]
  • VGF:VGF nerve growth factor inducible [Gene - OMIM - HGNC]
  • ZASP:ZO-2 associated speckle protein [Gene - OMIM]
  • ACHE:acetylcholinesterase (Yt blood group) [Gene - OMIM - HGNC]
  • ACTL6B:actin like 6B [Gene - OMIM - HGNC]
  • ARPC1B:actin related protein 2/3 complex subunit 1B [Gene - OMIM - HGNC]
  • AP1S1:adaptor related protein complex 1 subunit sigma 1 [Gene - OMIM - HGNC]
  • AP4M1:adaptor related protein complex 4 subunit mu 1 [Gene - OMIM - HGNC]
  • AZGP1:alpha-2-glycoprotein 1, zinc-binding [Gene - OMIM - HGNC]
  • CNPY4:canopy FGF signaling regulator 4 [Gene - OMIM - HGNC]
  • CPSF4:cleavage and polyadenylation specific factor 4 [Gene - OMIM - HGNC]
  • CYP3A43:cytochrome P450 family 3 subfamily A member 43 [Gene - OMIM - HGNC]
  • CYP3A4:cytochrome P450 family 3 subfamily A member 4 [Gene - OMIM - HGNC]
  • CYP3A5:cytochrome P450 family 3 subfamily A member 5 [Gene - OMIM - HGNC]
  • CYP3A7:cytochrome P450 family 3 subfamily A member 7 [Gene - OMIM - HGNC]
  • EPO:erythropoietin [Gene - OMIM - HGNC]
  • FAM200A:family with sequence similarity 200 member A [Gene - HGNC]
  • GAL3ST4:galactose-3-O-sulfotransferase 4 [Gene - OMIM - HGNC]
  • GJC3:gap junction protein gamma 3 [Gene - OMIM - HGNC]
  • GPC2:glypican 2 [Gene - OMIM - HGNC]
  • LAMTOR4:late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 [Gene - OMIM - HGNC]
  • LRCH4:leucine rich repeats and calponin homology domain containing 4 [Gene - OMIM - HGNC]
  • MBLAC1:metallo-beta-lactamase domain containing 1 [Gene - HGNC]
  • MEPCE:methylphosphate capping enzyme [Gene - OMIM - HGNC]
  • MIR106B:microRNA 106b [Gene - OMIM - HGNC]
  • MIR25:microRNA 25 [Gene - OMIM - HGNC]
  • MIR93:microRNA 93 [Gene - OMIM - HGNC]
  • MCM7:minichromosome maintenance complex component 7 [Gene - OMIM - HGNC]
  • MOGAT3:monoacylglycerol O-acyltransferase 3 [Gene - OMIM - HGNC]
  • MOSPD3:motile sperm domain containing 3 [Gene - OMIM - HGNC]
  • MUC12:mucin 12, cell surface associated [Gene - OMIM - HGNC]
  • MUC17:mucin 17, cell surface associated [Gene - OMIM - HGNC]
  • MUC3A:mucin 3A, cell surface associated [Gene - OMIM - HGNC]
  • NYAP1:neuronal tyrosine phosphorylated phosphoinositide-3-kinase adaptor 1 [Gene - OMIM - HGNC]
  • OR2AE1:olfactory receptor family 2 subfamily AE member 1 [Gene - HGNC]
  • PILRA:paired immunoglobin like type 2 receptor alpha [Gene - OMIM - HGNC]
  • PTCD1:pentatricopeptide repeat domain 1 [Gene - OMIM - HGNC]
  • PCOLCE:procollagen C-endopeptidase enhancer [Gene - OMIM - HGNC]
  • PLOD3:procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 [Gene - OMIM - HGNC]
  • PPP1R35:protein phosphatase 1 regulatory subunit 35 [Gene - OMIM - HGNC]
  • SERPINE1:serpin family E member 1 [Gene - OMIM - HGNC]
  • SRRT:serrate, RNA effector molecule [Gene - OMIM - HGNC]
  • SLC12A9:solute carrier family 12 member 9 [Gene - OMIM - HGNC]
  • SPDYE3:speedy/RINGO cell cycle regulator family member E3 [Gene - OMIM - HGNC]
  • SPACDR:sperm acrosome developmental regulator [Gene - OMIM - HGNC]
  • TRIP6:thyroid hormone receptor interactor 6 [Gene - OMIM - HGNC]
  • TRAPPC14:trafficking protein particle complex subunit 14 [Gene - OMIM - HGNC]
  • TFR2:transferrin receptor 2 [Gene - OMIM - HGNC]
  • TRIM4:tripartite motif containing 4 [Gene - HGNC]
  • TRIM56:tripartite motif containing 56 [Gene - OMIM - HGNC]
  • ZCWPW1:zinc finger CW-type and PWWP domain containing 1 [Gene - OMIM - HGNC]
  • ZSCAN21:zinc finger and SCAN domain containing 21 [Gene - OMIM - HGNC]
  • ZSCAN25:zinc finger and SCAN domain containing 25 [Gene - HGNC]
  • ZNF394:zinc finger protein 394 [Gene - OMIM - HGNC]
  • ZNF3:zinc finger protein 3 [Gene - OMIM - HGNC]
  • ZNF655:zinc finger protein 655 [Gene - OMIM - HGNC]
  • ZNF789:zinc finger protein 789 [Gene - HGNC]
  • ZKSCAN1:zinc finger with KRAB and SCAN domains 1 [Gene - OMIM - HGNC]
  • ZKSCAN5:zinc finger with KRAB and SCAN domains 5 [Gene - OMIM - HGNC]
  • ZAN:zonadhesin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q22.1
Genomic location:
Chr7: 98983338 - 100860555 (on Assembly GRCh37)
Preferred name:
NC_000007.13:g.(?_98983338)_(100860555_?)del
HGVS:
NC_000007.13:g.(?_98983338)_(100860555_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002142644Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 5, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV002142644.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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. This variant has not been reported in the literature in individuals affected with AP1S1-related conditions. A gross deletion of the genomic region encompassing the full coding sequence of the AP1S1 gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in AP1S1 cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

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

Last Updated: Jun 17, 2024