NC_000019.9:g.(?_54626515)_(54627192_?)del AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 7, 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:: RCV003119639.2

Allele description

NC_000019.9:g.(?_54626515)_(54627192_?)del

Gene:: PRPF31:pre-mRNA processing factor 31 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 19q13.42
Genomic location:: Chr19: 54626515 - 54627192 (on Assembly GRCh37)
Preferred name:: NC_000019.9:g.(?_54626515)_(54627192_?)del
HGVS:: NC_000019.9:g.(?_54626515)_(54627192_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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cleavage and polyadenylation specificity factor 73-I [Arabidopsis thaliana]
gi|30696512|ref|NP_849835.1|

Protein
type II 3-dehydroquinate dehydratase [Streptomyces phyllanthi]
type II 3-dehydroquinate dehydratase [Streptomyces phyllanthi]
gi|2638940196|ref|WP_322725788.1|

Protein
TCP domain protein 17 [Arabidopsis thaliana]
TCP domain protein 17 [Arabidopsis thaliana]
gi|15241512|ref|NP_196424.1|

Protein
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MeSH
Trimethoprim
Trimethoprim
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MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003794090	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 7, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 16199547, 18317597, 23950152, 30030392, 30360737, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003794090

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 7, 2022)

germline

clinical testing

PubMed (6)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Premature termination codons in PRPF31 cause retinitis pigmentosa via haploinsufficiency due to nonsense-mediated mRNA decay.

Rio Frio T, Wade NM, Ransijn A, Berson EL, Beckmann JS, Rivolta C.

J Clin Invest. 2008 Apr;118(4):1519-31. doi: 10.1172/JCI34211.

PubMed [citation]

PMID:: 18317597
PMCID:: PMC2262031

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV003794090.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant results in the deletion of exon 6 and part of exon 7 (c.421-318_592del) of the PRPF31 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PRPF31 are known to be pathogenic (PMID: 18317597, 23950152). This variant has not been reported in the literature in individuals affected with PRPF31-related conditions. This variant disrupts a region of the PRPF31 protein in which other variant(s) (p.Leu197Pro) have been determined to be pathogenic (PMID: 30030392, 30360737). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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: Mar 26, 2023

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