NC_000023.10:g.(?_152014869)_(155171615_?)del AND Creatine transporter deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 17, 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:: RCV003119103.3

Allele description [Variation Report for NC_000023.10:g.(?_152014869)_(155171615_?)del]

NC_000023.10:g.(?_152014869)_(155171615_?)del

Genes:

ABCD1:ATP binding cassette subfamily D member 1 [Gene - OMIM - HGNC]
ATP6AP1:ATPase H+ transporting accessory protein 1 [Gene - OMIM - HGNC]
ATP2B3:ATPase plasma membrane Ca2+ transporting 3 [Gene - OMIM - HGNC]
BCAP31:B cell receptor associated protein 31 [Gene - OMIM - HGNC]
BRCC3:BRCA1/BRCA2-containing complex subunit 3 [Gene - OMIM - HGNC]
CMC4:C-X9-C motif containing 4 [Gene - OMIM - HGNC]
FAM3A:FAM3 metabolism regulating signaling molecule A [Gene - OMIM - HGNC]
FUNDC2:FUN14 domain containing 2 [Gene - OMIM - HGNC]
GDI1:GDP dissociation inhibitor 1 [Gene - OMIM - HGNC]
GAB3:GRB2 associated binding protein 3 [Gene - OMIM - HGNC]
H2AB1:H2A.B variant histone 1 [Gene - OMIM - HGNC]
H2AB2:H2A.B variant histone 2 [Gene - OMIM - HGNC]
H2AB3:H2A.B variant histone 3 [Gene - OMIM - HGNC]
HAUS7:HAUS augmin like complex subunit 7 [Gene - OMIM - HGNC]
LAGE3:L antigen family member 3 [Gene - OMIM - HGNC]
L1CAM:L1 cell adhesion molecule [Gene - OMIM - HGNC]
MAGEA1:MAGE family member A1 [Gene - OMIM - HGNC]
MPP1:MAGUK p55 scaffold protein 1 [Gene - OMIM - HGNC]
NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
NSDHL:NAD(P) dependent steroid dehydrogenase-like [Gene - OMIM - HGNC]
PDZD4:PDZ domain containing 4 [Gene - OMIM - HGNC]
PNMA3:PNMA family member 3 [Gene - OMIM - HGNC]
PNMA5:PNMA family member 5 [Gene - OMIM - HGNC]
PNMA6A:PNMA family member 6A [Gene - OMIM - HGNC]
PNMA6E:PNMA family member 6E [Gene - HGNC]
RAB39B:RAB39B, member RAS oncogene family [Gene - OMIM - HGNC]
ARHGAP4:Rho GTPase activating protein 4 [Gene - OMIM - HGNC]
SRPK3:SRSF protein kinase 3 [Gene - OMIM - HGNC]
VBP1:VHL binding protein 1 [Gene - OMIM - HGNC]
ZFP92:ZFP92 zinc finger protein [Gene - HGNC]
AVPR2:arginine vasopressin receptor 2 [Gene - OMIM - HGNC]
BGN:biglycan [Gene - OMIM - HGNC]
CTAG1A:cancer/testis antigen 1A [Gene - OMIM - HGNC]
CTAG1B:cancer/testis antigen 1B [Gene - OMIM - HGNC]
CTAG2:cancer/testis antigen 2 [Gene - OMIM - HGNC]
CLIC2:chloride intracellular channel 2 [Gene - OMIM - HGNC]
F8A1:coagulation factor VIII associated 1 [Gene - OMIM - HGNC]
F8A2:coagulation factor VIII associated 2 [Gene - HGNC]
F8A3:coagulation factor VIII associated 3 [Gene - HGNC]
F8:coagulation factor VIII [Gene - OMIM - HGNC]
CCNQ:cyclin Q [Gene - OMIM - HGNC]
DNASE1L1:deoxyribonuclease 1 like 1 [Gene - OMIM - HGNC]
DUSP9:dual specificity phosphatase 9 [Gene - OMIM - HGNC]
DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
EMD:emerin [Gene - OMIM - HGNC]
FAM50A:family with sequence similarity 50 member A [Gene - OMIM - HGNC]
FLNA:filamin A [Gene - OMIM - HGNC]
G6PD:glucose-6-phosphate dehydrogenase [Gene - OMIM - HGNC]
HCFC1:host cell factor C1 [Gene - OMIM - HGNC]
IKBKG:inhibitor of nuclear factor kappa B kinase regulatory subunit gamma [Gene - OMIM - HGNC]
IRAK1:interleukin 1 receptor associated kinase 1 [Gene - OMIM - HGNC]
IDH3G:isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Gene - OMIM - HGNC]
MTCP1:mature T cell proliferation 1 [Gene - OMIM - HGNC]
MECP2:methyl-CpG binding protein 2 [Gene - OMIM - HGNC]
OPN1LW:opsin 1, long wave sensitive [Gene - OMIM - HGNC]
OPN1MW2:opsin 1, medium wave sensitive 2 [Gene - HGNC]
OPN1MW:opsin 1, medium wave sensitive [Gene - OMIM - HGNC]
PLXNA3:plexin A3 [Gene - OMIM - HGNC]
PLXNB3:plexin B3 [Gene - OMIM - HGNC]
PNCK:pregnancy up-regulated nonubiquitous CaM kinase [Gene - OMIM - HGNC]
RENBP:renin binding protein [Gene - OMIM - HGNC]
RPL10:ribosomal protein L10 [Gene - OMIM - HGNC]
SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]
SMIM9:small integral membrane protein 9 [Gene - HGNC]
SLC10A3:solute carrier family 10 member 3 [Gene - OMIM - HGNC]
SLC6A8:solute carrier family 6 member 8 [Gene - OMIM - HGNC]
TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]
TEX28:testis expressed 28 [Gene - OMIM - HGNC]
TREX2:three prime repair exonuclease 2 [Gene - OMIM - HGNC]
TKTL1:transketolase like 1 [Gene - OMIM - HGNC]
TMEM187:transmembrane protein 187 [Gene - OMIM - HGNC]
TMLHE:trimethyllysine hydroxylase, epsilon [Gene - OMIM - HGNC]
UBL4A:ubiquitin like 4A [Gene - OMIM - HGNC]
ZNF185:zinc finger protein 185 with LIM domain [Gene - OMIM - HGNC]
ZNF275:zinc finger protein 275 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

ChrX: 152014869 - 155171615 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_152014869)_(155171615_?)del

HGVS:

NC_000023.10:g.(?_152014869)_(155171615_?)del

Condition(s)

Name:: Creatine transporter deficiency (CCDS1)
Synonyms:: Creatine deficiency, X-linked; Mental retardation , X-linked with seizures, short stature and midface hypoplasia; Mental retardation , X-linked, with creatine transport deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010305; MedGen: C1845862; Orphanet: 52503; OMIM: 300352

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794848	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 17, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 22281021, 16601897, 23660394, 24962355, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794848

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 17, 2022)

germline

clinical testing

PubMed (5)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Detection of variants in SLC6A8 and functional analysis of unclassified missense variants.

Betsalel OT, Pop A, Rosenberg EH, Fernandez-Ojeda M; Creatine Transporter Research, Group., Jakobs C, Salomons GS.

Mol Genet Metab. 2012 Apr;105(4):596-601. doi: 10.1016/j.ymgme.2011.12.022. Epub 2012 Jan 6.

PubMed [citation]

PMID:: 22281021

X-linked creatine transporter defect: a report on two unrelated boys with a severe clinical phenotype.

Anselm IA, Alkuraya FS, Salomons GS, Jakobs C, Fulton AB, Mazumdar M, Rivkin M, Frye R, Poussaint TY, Marsden D.

J Inherit Metab Dis. 2006 Feb;29(1):214-9. Erratum in: J Inherit Metab Dis. 2006 Dec;29(6):764. Anselm, IM [corrected to Anselm, IA].

PubMed [citation]

PMID:: 16601897
PMCID:: PMC2393549

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003794848.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the SLC6A8 gene has been identified. Loss-of-function variants in SLC6A8 are known to be pathogenic (PMID: 22281021). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. A similar copy number variant has been observed in individual(s) with clinical features of creatinine transporter deficiency (PMID: 16601897, 23660394, 24962355). 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

Last Updated: May 26, 2024

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