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GRCh37/hg19 7q21.2-22.1(chr7:92445452-99686985)x1 AND Split hand-foot malformation 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 28, 2015
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:
RCV000656540.1

Allele description [Variation Report for GRCh37/hg19 7q21.2-22.1(chr7:92445452-99686985)x1]

GRCh37/hg19 7q21.2-22.1(chr7:92445452-99686985)x1

Genes:
  • ATP5MF:ATP synthase membrane subunit f [Gene - OMIM - HGNC]
  • ATP5MF-PTCD1:ATP5MF-PTCD1 readthrough [Gene - HGNC]
  • BAIAP2L1:BAR/IMD domain containing adaptor protein 2 like 1 [Gene - OMIM - HGNC]
  • BUD31:BUD31 homolog [Gene - OMIM - HGNC]
  • BET1:Bet1 golgi vesicular membrane trafficking protein [Gene - OMIM - HGNC]
  • CASD1:CAS1 domain containing 1 [Gene - OMIM - HGNC]
  • COPS6:COP9 signalosome subunit 6 [Gene - OMIM - HGNC]
  • GNG11:G protein subunit gamma 11 [Gene - OMIM - HGNC]
  • GNGT1:G protein subunit gamma transducin 1 [Gene - OMIM - HGNC]
  • HEPACAM2:HEPACAM family member 2 [Gene - OMIM - HGNC]
  • PDAP1:PDGFA associated protein 1 [Gene - OMIM - HGNC]
  • SEM1:SEM1 26S proteasome subunit [Gene - OMIM - HGNC]
  • SMURF1:SMAD specific E3 ubiquitin protein ligase 1 [Gene - OMIM - HGNC]
  • VPS50:VPS50 subunit of EARP/GARPII complex [Gene - OMIM - HGNC]
  • ARPC1A:actin related protein 2/3 complex subunit 1A [Gene - OMIM - HGNC]
  • ARPC1B:actin related protein 2/3 complex subunit 1B [Gene - OMIM - HGNC]
  • AZGP1:alpha-2-glycoprotein 1, zinc-binding [Gene - OMIM - HGNC]
  • ASB4:ankyrin repeat and SOCS box containing 4 [Gene - OMIM - HGNC]
  • ASNS:asparagine synthetase (glutamine-hydrolyzing) [Gene - OMIM - HGNC]
  • BHLHA15:basic helix-loop-helix family member a15 [Gene - OMIM - HGNC]
  • BRI3:brain protein I3 [Gene - OMIM - HGNC]
  • CALCR:calcitonin receptor [Gene - OMIM - HGNC]
  • C7orf76:chromosome 7 open reading frame 76 [Gene - HGNC]
  • CPSF4:cleavage and polyadenylation specific factor 4 [Gene - OMIM - HGNC]
  • COL1A2:collagen type I alpha 2 chain [Gene - OMIM - HGNC]
  • CDK6:cyclin dependent kinase 6 [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]
  • DLX5:distal-less homeobox 5 [Gene - OMIM - HGNC]
  • DLX6:distal-less homeobox 6 [Gene - OMIM - HGNC]
  • DYNC1I1:dynein cytoplasmic 1 intermediate chain 1 [Gene - OMIM - HGNC]
  • FAM200A:family with sequence similarity 200 member A [Gene - HGNC]
  • GJC3:gap junction protein gamma 3 [Gene - OMIM - HGNC]
  • KPNA7:karyopherin subunit alpha 7 [Gene - OMIM - HGNC]
  • LMTK2:lemur tyrosine kinase 2 [Gene - OMIM - HGNC]
  • MIR489:microRNA 489 [Gene - OMIM - HGNC]
  • NPTX2:neuronal pentraxin 2 [Gene - OMIM - HGNC]
  • OR2AE1:olfactory receptor family 2 subfamily AE member 1 [Gene - HGNC]
  • OCM2:oncomodulin 2 [Gene - HGNC]
  • PON1:paraoxonase 1 [Gene - OMIM - HGNC]
  • PON2:paraoxonase 2 [Gene - OMIM - HGNC]
  • PON3:paraoxonase 3 [Gene - OMIM - HGNC]
  • PEG10:paternally expressed 10 [Gene - OMIM - HGNC]
  • PTCD1:pentatricopeptide repeat domain 1 [Gene - OMIM - HGNC]
  • PPP1R9A:protein phosphatase 1 regulatory subunit 9A [Gene - OMIM - HGNC]
  • PDK4:pyruvate dehydrogenase kinase 4 [Gene - OMIM - HGNC]
  • SGCE:sarcoglycan epsilon [Gene - OMIM - HGNC]
  • SLC25A13:solute carrier family 25 member 13 [Gene - OMIM - HGNC]
  • SAMD9L:sterile alpha motif domain containing 9 like [Gene - OMIM - HGNC]
  • SAMD9:sterile alpha motif domain containing 9 [Gene - OMIM - HGNC]
  • SDHAF3:succinate dehydrogenase complex assembly factor 3 [Gene - OMIM - HGNC]
  • TAC1:tachykinin precursor 1 [Gene - OMIM - HGNC]
  • TECPR1:tectonin beta-propeller repeat containing 1 [Gene - OMIM - HGNC]
  • TFPI2:tissue factor pathway inhibitor 2 [Gene - OMIM - HGNC]
  • TRRAP:transformation/transcription domain associated protein [Gene - OMIM - HGNC]
  • TMEM130:transmembrane protein 130 [Gene - HGNC]
  • TRIM4:tripartite motif containing 4 [Gene - 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]
Variant type:
copy number loss
Cytogenetic location:
7q21.2-22.1
Genomic location:
Chr7: 92445452 - 99686985 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 7q21.2-22.1(chr7:92445452-99686985)x1
Other names:
arr[GRCh37]7q21.2q22.1(92445452_99686985)x1
HGVS:
    Observations:
    1

    Condition(s)

    Name:
    Split hand-foot malformation 1
    Synonyms:
    SPLIT-HAND DEFORMITY; SPLIT-HAND/FOOT DEFORMITY 1; Split-hand/foot malformation 1; See all synonyms [MedGen]
    Identifiers:
    MONDO: MONDO:0008464; MedGen: C2931019; Orphanet: 2440; OMIM: 183600

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV000778512Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences
    criteria provided, single submitter

    (ACMG Guidelines, 2013)    		Pathogenic
    (Sep 28, 2015)     		unknownclinical testing

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

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    North Indianunknownyes1not providednot providednot providednot providedclinical testing

    Citations

    PubMed

    ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013.

    South ST, Lee C, Lamb AN, Higgins AW, Kearney HM; Working Group for the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee..

    Genet Med. 2013 Nov;15(11):901-9. doi: 10.1038/gim.2013.129. Epub 2013 Sep 26.

    PubMed [citation]
    PMID:
    24071793

    Details of each submission

    From Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, SCV000778512.1

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1North Indian1not providednot providedclinical testing PubMed (1)

    Description

    CMA analysis revealed a deletion of 7.2Mb at chromosome 7q21.2. This region includes genes DYNC1I1, DLX5, DLX6, SLC25A13, SMAD9, PEG10, PPP1R9A, CDK6. This is a known region of split-hand/foot malformation-1 (SHFM1). Deletions of varying sizes are reported as pathogenic in ISCA and DECIPHER.

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1unknownyesnot providednot providednot provided1not providednot providednot provided

    Last Updated: Mar 26, 2023