NC_000016.9:g.(?_65821800)_(67208957_?)del AND Cataract 5 multiple types

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 18, 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:: RCV003107427.2

Allele description

NC_000016.9:g.(?_65821800)_(67208957_?)del

Genes:

CMTM1:CKLF like MARVEL transmembrane domain containing 1 [Gene - OMIM - HGNC]
CMTM2:CKLF like MARVEL transmembrane domain containing 2 [Gene - OMIM - HGNC]
CMTM3:CKLF like MARVEL transmembrane domain containing 3 [Gene - OMIM - HGNC]
CMTM4:CKLF like MARVEL transmembrane domain containing 4 [Gene - OMIM - HGNC]
CKLF-CMTM1:CKLF-CMTM1 readthrough [Gene - HGNC]
FBXL8:F-box and leucine rich repeat protein 8 [Gene - OMIM - HGNC]
NAE1:NEDD8 activating enzyme E1 subunit 1 [Gene - OMIM - HGNC]
RRAD:RRAD, Ras related glycolysis inhibitor and calcium channel regulator [Gene - OMIM - HGNC]
TRADD:TNFRSF1A associated via death domain [Gene - OMIM - HGNC]
B3GNT9:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 [Gene - HGNC]
BEAN1:brain expressed associated with NEDD4 1 [Gene - OMIM - HGNC]
CDH16:cadherin 16 [Gene - OMIM - HGNC]
CDH5:cadherin 5 [Gene - OMIM - HGNC]
CA7:carbonic anhydrase 7 [Gene - OMIM - HGNC]
CES2:carboxylesterase 2 [Gene - OMIM - HGNC]
CES3:carboxylesterase 3 [Gene - OMIM - HGNC]
CES4A:carboxylesterase 4A [Gene - HGNC]
CKLF:chemokine like factor [Gene - OMIM - HGNC]
CBFB:core-binding factor subunit beta [Gene - OMIM - HGNC]
CIAO2B:cytosolic iron-sulfur assembly component 2B [Gene - OMIM - HGNC]
DYNC1LI2:dynein cytoplasmic 1 light intermediate chain 2 [Gene - OMIM - HGNC]
HSF4:heat shock transcription factor 4 [Gene - OMIM - HGNC]
NOL3:nucleolar protein 3 [Gene - OMIM - HGNC]
PHAF1:phagosome assembly factor 1 [Gene - HGNC]
PDP2:pyruvate dehydrogenase phosphatase catalytic subunit 2 [Gene - OMIM - HGNC]
TERB1:telomere repeat binding bouquet formation protein 1 [Gene - OMIM - HGNC]
TK2:thymidine kinase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q21-22.1

Genomic location:

Chr16: 65821800 - 67208957 (on Assembly GRCh37)

Preferred name:

NC_000016.9:g.(?_65821800)_(67208957_?)del

HGVS:

NC_000016.9:g.(?_65821800)_(67208957_?)del

Condition(s)

Name:: Cataract 5 multiple types (CTRCT5)
Synonyms:: Perinuclear cataract; CATARACT, MARNER TYPE; CATARACT 5, LAMELLAR; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007290; MedGen: C0266537; Orphanet: 91492; OMIM: 116800; Human Phenotype Ontology: HP:0007971

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003793609	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 18, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15959809, 23329665, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003793609

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 18, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Locus heterogeneity in autosomal recessive congenital cataracts: linkage to 9q and germline HSF4 mutations.

Forshew T, Johnson CA, Khaliq S, Pasha S, Willis C, Abbasi R, Tee L, Smith U, Trembath RC, Mehdi SQ, Moore AT, Maher ER.

Hum Genet. 2005 Sep;117(5):452-9. Epub 2005 Jun 16.

PubMed [citation]

PMID:: 15959809

Copy number variations of DNA repair genes and the age-related cataract: Jiangsu Eye Study.

Jiang J, Zhou J, Yao Y, Zhu R, Liang C, Jiang S, Yang M, Lu Y, Xing Q, Guan H.

Invest Ophthalmol Vis Sci. 2013 Feb 1;54(2):932-8. doi: 10.1167/iovs.12-10948.

PubMed [citation]

PMID:: 23329665

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003793609.1

#	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 HSF4 gene has been identified. Loss-of-function variants in HSF4 are known to be pathogenic (PMID: 15959809). 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 age-related cataract (PMID: 23329665). 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: Nov 11, 2023

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