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NM_006346.4(PIBF1):c.1056_1068del (p.Lys353fs) AND Joubert syndrome 33

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 25, 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:
RCV002810038.3

Allele description [Variation Report for NM_006346.4(PIBF1):c.1056_1068del (p.Lys353fs)]

NM_006346.4(PIBF1):c.1056_1068del (p.Lys353fs)

Gene:
PIBF1:progesterone immunomodulatory binding factor 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q22.1
Genomic location:
Preferred name:
NM_006346.4(PIBF1):c.1056_1068del (p.Lys353fs)
Other names:
NR_146206.2:n.1320_1332del
HGVS:
  • NC_000013.11:g.72827873_72827885del
  • NG_053118.1:g.50850_50862del
  • NG_053118.2:g.50742_50754del
  • NM_001349655.2:c.1056_1068del
  • NM_006346.4:c.1056_1068delMANE SELECT
  • NP_001336584.1:p.Lys353fs
  • NP_006337.2:p.Lys353fs
  • NC_000013.10:g.73402011_73402023del
  • NR_146205.2:n.1320_1332del
  • NR_146206.2:n.1320_1332del
Protein change:
K353fs
Molecular consequence:
  • NM_001349655.2:c.1056_1068del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_006346.4:c.1056_1068del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_146205.2:n.1320_1332del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146206.2:n.1320_1332del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Joubert syndrome 33
Identifiers:
MONDO: MONDO:0033311; MedGen: C4540389; OMIM: 617767

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003761333Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 25, 2023) 		germlinecuration

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761333.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The heterozygous p.Lys353ArgfsTer7 variant in PIBF1 was identified by our study, in the compound heterozygous state with a likely pathogenic variant (dbSNP ID: rs751380401), in one individual with Joubert syndrome. Trio exome analysis revealed that this variant was in trans with a likely pathogenic variant (dbSNP ID: rs751380401). The p.Lys353ArgfsTer7 variant in PIBF1 has not been previously reported in individuals with Joubert syndrome 33. This variant was absent from large population studies. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 353 and leads to a premature termination codon 7 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the PIBF1 gene is strongly associated to autosomal recessive Joubert syndrome 33. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive Joubert syndrome 33. ACMG/AMP Criteria applied: PVS1_Strong, PM2_Supporting, PM3 (Richards 2015).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024