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NC_000001.10:g.(?_112318699)_(115576848_?)del AND Hereditary spastic paraplegia 47

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 2, 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:
RCV003109541.3

Allele description [Variation Report for NC_000001.10:g.(?_112318699)_(115576848_?)del]

NC_000001.10:g.(?_112318699)_(115576848_?)del

Genes:
  • BCAS2:BCAS2 pre-mRNA processing factor [Gene - OMIM - HGNC]
  • BCL2L15:BCL2 like 15 [Gene - OMIM - HGNC]
  • CTTNBP2NL:CTTNBP2 N-terminal like [Gene - OMIM - HGNC]
  • DENND2C:DENN domain containing 2C [Gene - HGNC]
  • DCLRE1B:DNA cross-link repair 1B [Gene - OMIM - HGNC]
  • MOV10:Mov10 RNA helicase [Gene - OMIM - HGNC]
  • NRAS:NRAS proto-oncogene, GTPase [Gene - OMIM - HGNC]
  • TAFA3:TAFA chemokine like family member 3 [Gene - OMIM - HGNC]
  • WNT2B:Wnt family member 2B [Gene - OMIM - HGNC]
  • AP4B1:adaptor related protein complex 4 subunit beta 1 [Gene - OMIM - HGNC]
  • AMPD1:adenosine monophosphate deaminase 1 [Gene - OMIM - HGNC]
  • CAPZA1:capping actin protein of muscle Z-line subunit alpha 1 [Gene - OMIM - HGNC]
  • CSDE1:cold shock domain containing E1 [Gene - OMIM - HGNC]
  • HIPK1:homeodomain interacting protein kinase 1 [Gene - OMIM - HGNC]
  • LRIG2:leucine rich repeats and immunoglobulin like domains 2 [Gene - OMIM - HGNC]
  • MAGI3:membrane associated guanylate kinase, WW and PDZ domain containing 3 [Gene - OMIM - HGNC]
  • OLFML3:olfactomedin like 3 [Gene - OMIM - HGNC]
  • KCND3:potassium voltage-gated channel subfamily D member 3 [Gene - OMIM - HGNC]
  • PPM1J:protein phosphatase, Mg2+/Mn2+ dependent 1J [Gene - OMIM - HGNC]
  • PTPN22:protein tyrosine phosphatase non-receptor type 22 [Gene - OMIM - HGNC]
  • PHTF1:putative homeodomain transcription factor 1 [Gene - OMIM - HGNC]
  • RHOC:ras homolog family member C [Gene - OMIM - HGNC]
  • RSBN1:round spermatid basic protein 1 [Gene - OMIM - HGNC]
  • SLC16A1:solute carrier family 16 member 1 [Gene - OMIM - HGNC]
  • ST7L:suppression of tumorigenicity 7 like [Gene - OMIM - HGNC]
  • SIKE1:suppressor of IKBKE 1 [Gene - OMIM - HGNC]
  • SYCP1:synaptonemal complex protein 1 [Gene - OMIM - HGNC]
  • SYT6:synaptotagmin 6 [Gene - OMIM - HGNC]
  • TSHB:thyroid stimulating hormone subunit beta [Gene - OMIM - HGNC]
  • TRIM33:tripartite motif containing 33 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p13.2
Genomic location:
Chr1: 112318699 - 115576848 (on Assembly GRCh37)
Preferred name:
NC_000001.10:g.(?_112318699)_(115576848_?)del
HGVS:
NC_000001.10:g.(?_112318699)_(115576848_?)del

Condition(s)

Name:
Hereditary spastic paraplegia 47
Synonyms:
Cerebral palsy, spastic quadriplegic, 5; adaptor protein 4 (AP-4) deficiency syndrome; Spastic paraplegia 47, autosomal recessive
Identifiers:
MONDO: MONDO:0013551; MedGen: C3279738; Orphanet: 280763; OMIM: 614066

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003791522Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 2, 2022) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutation in the AP4B1 gene cause hereditary spastic paraplegia type 47 (SPG47) .

Bauer P, Leshinsky-Silver E, Blumkin L, Schlipf N, Schröder C, Schicks J, Lev D, Riess O, Lerman-Sagie T, Schöls L.

Neurogenetics. 2012 Feb;13(1):73-6. doi: 10.1007/s10048-012-0314-0.

PubMed [citation]
PMID:
22290197

Autosomal recessive spastic tetraplegia caused by AP4M1 and AP4B1 gene mutation: expansion of the facial and neuroimaging features.

Tüysüz B, Bilguvar K, Koçer N, Yalçınkaya C, Çağlayan O, Gül E, Sahin S, Çomu S, Günel M.

Am J Med Genet A. 2014 Jul;164A(7):1677-85. doi: 10.1002/ajmg.a.36514. Epub 2014 Apr 3.

PubMed [citation]
PMID:
24700674
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV003791522.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the AP4B1 gene has been identified. Loss-of-function variants in AP4B1 are known to be pathogenic (PMID: 22290197, 24700674, 24781758). 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 AP4B1-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 11, 2023