NC_000023.10:g.(?_14027032)_(19854400_?)del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 24, 2023
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:: RCV004583528.1

Allele description

NC_000023.10:g.(?_14027032)_(19854400_?)del

Genes:

BEND2:BEN domain containing 2 [Gene - HGNC]
BMX:BMX non-receptor tyrosine kinase [Gene - OMIM - HGNC]
CTPS2:CTP synthase 2 [Gene - OMIM - HGNC]
FANCB:FA complementation group B [Gene - OMIM - HGNC]
MAGEB17:MAGE family member B17 [Gene - OMIM - HGNC]
NHS:NHS actin remodeling regulator [Gene - OMIM - HGNC]
REPS2:RALBP1 associated Eps domain containing 2 [Gene - OMIM - HGNC]
RBBP7:RB binding protein 7, chromatin remodeling factor [Gene - OMIM - HGNC]
S100G:S100 calcium binding protein G [Gene - OMIM - HGNC]
SH3KBP1:SH3 domain containing kinase binding protein 1 [Gene - OMIM - HGNC]
SCML1:Scm polycomb group protein like 1 [Gene - OMIM - HGNC]
SCML2:Scm polycomb group protein like 2 [Gene - OMIM - HGNC]
AP1S2:adaptor related protein complex 1 subunit sigma 2 [Gene - OMIM - HGNC]
ADGRG2:adhesion G protein-coupled receptor G2 [Gene - OMIM - HGNC]
ACE2:angiotensin converting enzyme 2 [Gene - OMIM - HGNC]
ASB11:ankyrin repeat and SOCS box containing 11 [Gene - OMIM - HGNC]
ASB9:ankyrin repeat and SOCS box containing 9 [Gene - OMIM - HGNC]
CA5B:carbonic anhydrase 5B [Gene - OMIM - HGNC]
CLTRN:collectrin, amino acid transport regulator [Gene - OMIM - HGNC]
CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
GRPR:gastrin releasing peptide receptor [Gene - OMIM - HGNC]
GEMIN8:gem nuclear organelle associated protein 8 [Gene - OMIM - HGNC]
GLRA2:glycine receptor alpha 2 [Gene - OMIM - HGNC]
INE2:inactivation escape 2 [Gene - OMIM - HGNC]
MAP3K15:mitogen-activated protein kinase kinase kinase 15 [Gene - OMIM - HGNC]
MOSPD2:motile sperm domain containing 2 [Gene - OMIM - HGNC]
PIGA:phosphatidylinositol glycan anchor biosynthesis class A [Gene - OMIM - HGNC]
PHKA2:phosphorylase kinase regulatory subunit alpha 2 [Gene - OMIM - HGNC]
PIR:pirin [Gene - OMIM - HGNC]
PPEF1:protein phosphatase with EF-hand domain 1 [Gene - OMIM - HGNC]
PDHA1:pyruvate dehydrogenase E1 subunit alpha 1 [Gene - OMIM - HGNC]
RAI2:retinoic acid induced 2 [Gene - OMIM - HGNC]
RS1:retinoschisin 1 [Gene - OMIM - HGNC]
SYAP1:synapse associated protein 1 [Gene - HGNC]
TXLNG:taxilin gamma [Gene - OMIM - HGNC]
VEGFD:vascular endothelial growth factor D [Gene - OMIM - HGNC]
ZRSR2:zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp22.2-22.12

Genomic location:

ChrX: 14027032 - 19854400 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_14027032)_(19854400_?)del

HGVS:

NC_000023.10:g.(?_14027032)_(19854400_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005064634	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 24, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9618178, 17172462, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064634

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 24, 2023)

unknown

clinical testing

PubMed (3)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Functional implications of the spectrum of mutations found in 234 cases with X-linked juvenile retinoschisis. The Retinoschisis Consortium.

[No authors listed]

Hum Mol Genet. 1998 Jul;7(7):1185-92.

PubMed [citation]

PMID:: 9618178

X-linked retinoschisis: an update.

Sikkink SK, Biswas S, Parry NR, Stanga PE, Trump D.

J Med Genet. 2007 Apr;44(4):225-32. Epub 2006 Dec 15. Review.

PubMed [citation]

PMID:: 17172462
PMCID:: PMC2598044

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV005064634.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the RS1 gene has been identified. Loss-of-function variants in RS1 are known to be pathogenic (PMID: 9618178, 17172462). 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 RS1-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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 7, 2024

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