NM_207346.3(TSEN54):c.940del (p.Leu314fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 1, 2017
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:: RCV000680133.2

Allele description [Variation Report for NM_207346.3(TSEN54):c.940del (p.Leu314fs)]

NM_207346.3(TSEN54):c.940del (p.Leu314fs)

Gene:

TSEN54:tRNA splicing endonuclease subunit 54 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_207346.3(TSEN54):c.940del (p.Leu314fs)

HGVS:

NC_000017.11:g.75522021del
NG_013041.1:g.10494del
NM_207346.3:c.940delMANE SELECT
NP_997229.2:p.Leu314fs
NC_000017.10:g.73518100del
NC_000017.10:g.73518102del
NM_207346.2:c.938delC

Protein change:

L314fs

Links:

dbSNP: rs1012275384

NCBI 1000 Genomes Browser:

rs1012275384

Molecular consequence:

NM_207346.3:c.940del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Pontocerebellar hypoplasia type 4 (PCH4)
Synonyms:: Encephalopathy fatal infantile with olivopontocerebellar hypoplasia
Identifiers:: MONDO: MONDO:0009166; MedGen: C1856974; Orphanet: 166063; OMIM: 225753

Name:: Pontocerebellar hypoplasia type 2A (PCH2A)
Synonyms:: PONTOCEREBELLAR HYPOPLASIA WITH PROGRESSIVE CEREBRAL ATROPHY; VOLENDAM NEURODEGENERATIVE DISEASE
Identifiers:: MONDO: MONDO:0010190; MedGen: C1848526; Orphanet: 2524; OMIM: 277470

Recent activity

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uncharacterized protein AT2G04235 [Arabidopsis thaliana]
uncharacterized protein AT2G04235 [Arabidopsis thaliana]
gi|240254436|ref|NP_671774.4|

Protein
Homo sapiens a disintegrin and metalloproteinase domain 21 (ADAM21), mRNA
Homo sapiens a disintegrin and metalloproteinase domain 21 (ADAM21), mRNA
gi|11497039|ref|NM_003813.1|

Nucleotide
il17rd.S interleukin 17 receptor D S homeolog [Xenopus laevis]
il17rd.S interleukin 17 receptor D S homeolog [Xenopus laevis]
Gene ID:115597775

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000807577	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 1, 2017)	maternal	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 25326635

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000807577

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 1, 2017)

maternal

clinical testing

PubMed (2)
[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	maternal	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

Molecular findings among patients referred for clinical whole-exome sequencing.

Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, Chiang T, Leduc M, Beuten J, Zhang J, He W, Scull J, Willis A, Landsverk M, Craigen WJ, Bekheirnia MR, et al.

JAMA. 2014 Nov 12;312(18):1870-9. doi: 10.1001/jama.2014.14601.

PubMed [citation]

PMID:: 25326635
PMCID:: PMC4326249

Details of each submission

From Baylor Genetics, SCV000807577.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing (GTR000508680.4)	PubMed (2)

Description

This frameshift variant is categorized as deleterious according to ACMG guidelines (PMID:18414213) and was found once in our laboratory in trans with another pathogenic variant (A307S) in a 1-year-old female with pontocerebellar hypoplasia.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided	(GTR000508680.4)	not provided	not provided	not provided	not provided

Last Updated: Mar 5, 2024

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