NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser) AND multiple conditions

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Oct 18, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001813937.9

Allele description [Variation Report for NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser)]

NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_207346.3(TSEN54):c.919G>T (p.Ala307Ser)

HGVS:

NC_000017.11:g.75522000G>T
NG_013041.1:g.10473G>T
NM_207346.3:c.919G>TMANE SELECT
NP_997229.2:p.Ala307Ser
NC_000017.10:g.73518081G>T
NM_207346.2:c.919G>T
Q7Z6J9:p.Ala307Ser

Protein change:

A307S; ALA307SER

Links:

UniProtKB: Q7Z6J9#VAR_054813; OMIM: 608755.0001; OMIM: 608755.0002; dbSNP: rs113994152

NCBI 1000 Genomes Browser:

rs113994152

Molecular consequence:

NM_207346.3:c.919G>T - missense variant - [Sequence Ontology: SO:0001583]

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

Name:: Pontocerebellar hypoplasia type 5 (PCH5)
Synonyms:: Olivopontocerebellar hypoplasia fetal-onset
Identifiers:: MONDO: MONDO:0012438; MedGen: C1857762; Orphanet: 166068; OMIM: 610204

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000611245	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 28, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002061384	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 18, 2024)	germline	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

SCV000611245

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 28, 2021)

unknown

clinical testing

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

SCV002061384

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 18, 2024)

germline

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	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	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 Fulgent Genetics, Fulgent Genetics, SCV000611245.2

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

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

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV002061384.3

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

Description

PM3_Very Strong, PP1_Strong

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

Last Updated: Nov 10, 2024

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