NM_020320.5(RARS2):c.176_177del (p.Pro59fs) AND Pontocerebellar hypoplasia type 6

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 17, 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:: RCV003463471.1

Allele description [Variation Report for NM_020320.5(RARS2):c.176_177del (p.Pro59fs)]

NM_020320.5(RARS2):c.176_177del (p.Pro59fs)

Gene:

RARS2:arginyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6q15

Genomic location:

Preferred name:

NM_020320.5(RARS2):c.176_177del (p.Pro59fs)

HGVS:

NC_000006.12:g.87564166_87564167del
NG_008601.1:g.30851_30852del
NM_001318785.2:c.-294_-293del
NM_001350505.2:c.176_177del
NM_001350506.2:c.-350_-349del
NM_001350507.2:c.-350_-349del
NM_001350508.2:c.-512_-511del
NM_001350509.2:c.-294_-293del
NM_001350510.2:c.-350_-349del
NM_001350511.2:c.-350_-349del
NM_020320.5:c.176_177delMANE SELECT
NP_001337434.1:p.Pro59fs
NP_064716.2:p.Pro59fs
NC_000006.11:g.88273884_88273885del
NR_134857.2:n.206_207del
NR_146738.2:n.427_428del
NR_146739.2:n.427_428del
NR_146740.2:n.427_428del
NR_146741.2:n.353_354del
NR_146742.2:n.427_428del
NR_146743.2:n.427_428del
NR_146744.2:n.427_428del
NR_146745.2:n.427_428del
NR_146746.2:n.645_646del
NR_146747.2:n.206_207del
NR_146748.2:n.427_428del
NR_146749.2:n.427_428del
NR_146750.2:n.427_428del
NR_146751.2:n.427_428del
NR_146752.2:n.427_428del
NR_146753.2:n.427_428del
NR_146754.2:n.427_428del
NR_146755.2:n.427_428del
NR_146756.2:n.206_207del
NR_146757.2:n.353_354del
NR_146758.2:n.427_428del
NR_146759.2:n.427_428del

Protein change:

P59fs

Molecular consequence:

NM_001318785.2:c.-294_-293del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350506.2:c.-350_-349del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350507.2:c.-350_-349del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350508.2:c.-512_-511del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350509.2:c.-294_-293del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350510.2:c.-350_-349del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350511.2:c.-350_-349del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350505.2:c.176_177del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_020320.5:c.176_177del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_134857.2:n.206_207del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146738.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146739.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146740.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146741.2:n.353_354del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146742.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146743.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146744.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146745.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146746.2:n.645_646del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146747.2:n.206_207del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146748.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146749.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146750.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146751.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146752.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146753.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146754.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146755.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146756.2:n.206_207del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146757.2:n.353_354del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146758.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146759.2:n.427_428del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Pontocerebellar hypoplasia type 6 (PCH6)
Synonyms:: Encephalopathy fatal infantile with mitochondrial respiratory chain defects
Identifiers:: MONDO: MONDO:0012683; MedGen: C1969084; Orphanet: 166073; OMIM: 611523

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004208465	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 17, 2023)	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

SCV004208465

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 17, 2023)

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	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 Baylor Genetics, SCV004208465.1

#	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

Last Updated: Dec 30, 2023

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