NC_000023.10:g.(?_12885698)_(13787227_?)del AND multiple conditions

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 24, 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:: RCV003122295.2

Allele description

NC_000023.10:g.(?_12885698)_(13787227_?)del

Genes:

EGFL6:EGF like domain multiple 6 [Gene - OMIM - HGNC]
OFD1:OFD1 centriole and centriolar satellite protein [Gene - OMIM - HGNC]
RAB9A:RAB9A, member RAS oncogene family [Gene - OMIM - HGNC]
ATXN3L:ataxin 3 like [Gene - OMIM - HGNC]
FAM9C:family with sequence similarity 9 member C [Gene - OMIM - HGNC]
TMSB4X:thymosin beta 4 X-linked [Gene - OMIM - HGNC]
TLR7:toll like receptor 7 [Gene - OMIM - HGNC]
TLR8:toll like receptor 8 [Gene - OMIM - HGNC]
TRAPPC2:trafficking protein particle complex subunit 2 [Gene - OMIM - HGNC]
TCEANC:transcription elongation factor A N-terminal and central domain containing [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp22.2

Genomic location:

ChrX: 12885698 - 13787227 (on Assembly GRCh37)

Preferred name:

NC_000023.10:g.(?_12885698)_(13787227_?)del

HGVS:

NC_000023.10:g.(?_12885698)_(13787227_?)del

Condition(s)

Name:: Familial aplasia of the vermis
Synonyms:: CEREBELLOPARENCHYMAL DISORDER IV; Joubert syndrome; Cerebelloparenchymal disorder 4; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018772; MedGen: C0431399; Orphanet: 475; OMIM: PS213300

Name:: Orofaciodigital syndrome I (OFD1)
Synonyms:: OFDS I; Orofaciodigital syndrome 1; OFD syndrome 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010702; MedGen: C1510460; Orphanet: 2750; OMIM: 311200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791376	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 24, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16783569, 18546297, 27081566, 23033313, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791376

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 24, 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

A novel X-linked recessive mental retardation syndrome comprising macrocephaly and ciliary dysfunction is allelic to oral-facial-digital type I syndrome.

Budny B, Chen W, Omran H, Fliegauf M, Tzschach A, Wisniewska M, Jensen LR, Raynaud M, Shoichet SA, Badura M, Lenzner S, Latos-Bielenska A, Ropers HH.

Hum Genet. 2006 Sep;120(2):171-8. Epub 2006 Jun 17.

PubMed [citation]

PMID:: 16783569

Mutational spectrum of the oral-facial-digital type I syndrome: a study on a large collection of patients.

Prattichizzo C, Macca M, Novelli V, Giorgio G, Barra A, Franco B; Oral-Facial-Digital Type I (OFDI) Collaborative Group.

Hum Mutat. 2008 Oct;29(10):1237-46. doi: 10.1002/humu.20792.

PubMed [citation]

PMID:: 18546297

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003791376.1

#	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 OFD1 gene has been identified. Loss-of-function variants in OFD1 are known to be pathogenic (PMID: 16783569, 18546297, 27081566). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of OFD1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 23033313). 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: Jun 10, 2023

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