NM_003611.3(OFD1):c.121C>T (p.Arg41Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 24, 2020
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:: RCV001383219.15

Allele description [Variation Report for NM_003611.3(OFD1):c.121C>T (p.Arg41Ter)]

NM_003611.3(OFD1):c.121C>T (p.Arg41Ter)

Gene:

OFD1:OFD1 centriole and centriolar satellite protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp22.2

Genomic location:

Preferred name:

NM_003611.3(OFD1):c.121C>T (p.Arg41Ter)

HGVS:

NC_000023.11:g.13736487C>T
NG_008872.1:g.6775C>T
NG_011555.1:g.3137G>A
NM_001330209.2:c.121C>T
NM_001330210.2:c.-425C>T
NM_003611.3:c.121C>TMANE SELECT
NP_001317138.1:p.Arg41Ter
NP_003602.1:p.Arg41Ter
NC_000023.10:g.13754606C>T

Protein change:

R41*

Links:

dbSNP: rs312262810

NCBI 1000 Genomes Browser:

rs312262810

Molecular consequence:

NM_001330210.2:c.-425C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001330209.2:c.121C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_003611.3:c.121C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001582305	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 24, 2020)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16783569, 18546297, 27081566, 11179005, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001582305

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 24, 2020)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001582305.4

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

Description

This sequence change creates a premature translational stop signal (p.Arg41*) in the OFD1 gene. It is expected to result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in OFD1 are known to be pathogenic (PMID: 16783569, 18546297, 27081566). This variant has been observed in individual(s) with oral-facial-digital syndrome (PMID: 11179005). ClinVar contains an entry for this variant (Variation ID: 41066). This variant is not present in population databases (ExAC no frequency).

#	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 3, 2024

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