NM_004698.4(PRPF3):c.1481C>T (p.Thr494Met) AND Retinitis pigmentosa

Germline classification:: Uncertain significance (2 submissions)
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:: RCV001003129.3

Allele description [Variation Report for NM_004698.4(PRPF3):c.1481C>T (p.Thr494Met)]

NM_004698.4(PRPF3):c.1481C>T (p.Thr494Met)

Gene:

PRPF3:pre-mRNA processing factor 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.2

Genomic location:

Preferred name:

NM_004698.4(PRPF3):c.1481C>T (p.Thr494Met)

HGVS:

NC_000001.11:g.150344216C>T
NG_008245.1:g.27765C>T
NM_001350529.1:c.1076C>T
NM_004698.4:c.1481C>TMANE SELECT
NP_001337458.1:p.Thr359Met
NP_004689.1:p.Thr494Met
NC_000001.10:g.150316692C>T
NM_004698.2:c.1481C>T
NR_146766.1:n.1654C>T
NR_146767.1:n.1750C>T
NR_146768.1:n.1654C>T
NR_146769.1:n.1649C>T
O43395:p.Thr494Met

Protein change:

T359M; THR494MET

Links:

UniProtKB: O43395#VAR_016877; OMIM: 607301.0001; dbSNP: rs121434241

NCBI 1000 Genomes Browser:

rs121434241

Molecular consequence:

NM_001350529.1:c.1076C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004698.4:c.1481C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_146766.1:n.1654C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146767.1:n.1750C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146768.1:n.1654C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146769.1:n.1649C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001161198	Sharon lab, Hadassah-Hebrew University Medical Center	no assertion criteria provided	Pathogenic (Jun 23, 2019)	inherited	research
SCV001450576	Department of Genetics, Fundacion Jimenez Diaz University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001161198

Sharon lab, Hadassah-Hebrew University Medical Center

no assertion criteria provided

Pathogenic
(Jun 23, 2019)

inherited

research

SCV001450576

Department of Genetics, Fundacion Jimenez Diaz University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

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 Sharon lab, Hadassah-Hebrew University Medical Center, SCV001161198.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Department of Genetics, Fundacion Jimenez Diaz University Hospital, SCV001450576.1

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

Description

Variant not found in population databases, predicted deleterious by in-silico pathogenicity predictors, and previously reported in literature (PMID: 27898983). (ACMG: PM2 Moderate, PP3 Supporting; PP5 Supporting)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 30, 2024

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