chrX-13739016-TAAAG-T

Variant names:

• chrX-13739016-TAAAG-T
• rs312262830
• NM_003611.3:c.400_403delGAAA

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_003611.3(OFD1):​c.400_403delGAAA​(p.Glu134IlefsTer10) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 23)
• Consequence: OFD1 NM_003611.3 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 6.81
• Publications: 6 publications found

Genes affected

OFD1 (HGNC:2567): (OFD1 centriole and centriolar satellite protein) This gene is located on the X chromosome and encodes a centrosomal protein. A knockout mouse model has been used to study the effect of mutations in this gene. The mouse gene is also located on the X chromosome, however, unlike the human gene it is not subject to X inactivation. Mutations in this gene are associated with oral-facial-digital syndrome type I and Simpson-Golabi-Behmel syndrome type 2. Many pseudogenes have been identified; a single pseudogene is found on chromosome 5 while as many as fifteen have been found on the Y chromosome. [provided by RefSeq, Aug 2016]

OFD1 Gene-Disease associations (from GenCC):

• ciliopathy

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• Joubert syndrome 10

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• orofaciodigital syndrome I

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
• retinitis pigmentosa 23

  Inheritance: XL Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• retinitis pigmentosa

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• orofaciodigital syndrome type 6

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Simpson-Golabi-Behmel syndrome type 2

  Inheritance: XL Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-13739016-TAAAG-T is Pathogenic according to our data. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-13739016-TAAAG-T is described in CliVar as Pathogenic. Clinvar id is 41117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OFD1	NM_003611.3	c.400_403delGAAA	p.Glu134IlefsTer10	frameshift_variant	Exon 5 of 23	ENST00000340096.11	NP_003602.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OFD1	ENST00000340096.11	c.400_403delGAAA	p.Glu134IlefsTer10	frameshift_variant	Exon 5 of 23	1	NM_003611.3	ENSP00000344314.6

Frequencies

GnomAD3 genomes Cov.: 23

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 13, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joubert syndrome;C1510460:Orofaciodigital syndrome I Pathogenic:1

Nov 27, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Glu134Ilefs*10) in the OFD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OFD1 are known to be pathogenic (PMID: 16783569, 18546297, 27081566). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with oral-facial-digital syndrome (PMID: 18546297). ClinVar contains an entry for this variant (Variation ID: 41117). For these reasons, this variant has been classified as Pathogenic. -

Joubert syndrome 10 Pathogenic:1

Jun 25, 2017

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

De novo variant in proband, maternity and paternity confirmed (PS2). Previously reported pathogenic in 2 manuscripts but unclear if same patient described (PMID: 18546297; PMID: 24884629). Protein truncating variants are a known disease mechainism (PVS1) and absent from gnomAD (PM2). -

Retinitis pigmentosa 23;C1510460:Orofaciodigital syndrome I;C1846175:Simpson-Golabi-Behmel syndrome type 2;C2749019:Joubert syndrome 10 Pathogenic:1

Apr 03, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Orofaciodigital syndrome I;C1846175:Simpson-Golabi-Behmel syndrome type 2;C2749019:Joubert syndrome 10 Pathogenic:1

Dec 31, 2017

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.8
Mutation Taster		=2/198	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs312262830; hg19: chrX-13757135;