NM_020320.5(RARS2):c.472_474del (p.Lys158del) AND Pontocerebellar hypoplasia type 6

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Apr 9, 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:: RCV000850512.8

Allele description [Variation Report for NM_020320.5(RARS2):c.472_474del (p.Lys158del)]

NM_020320.5(RARS2):c.472_474del (p.Lys158del)

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.472_474del (p.Lys158del)

HGVS:

NC_000006.12:g.87545677_87545679del
NG_008601.1:g.49339_49341del
NM_001318785.2:c.-54_-52del
NM_001350505.2:c.472_474del
NM_001350506.2:c.-54_-52del
NM_001350507.2:c.-54_-52del
NM_001350508.2:c.-54_-52del
NM_001350509.2:c.-54_-52del
NM_001350510.2:c.-54_-52del
NM_001350511.2:c.-54_-52del
NM_020320.5:c.472_474delMANE SELECT
NP_001337434.1:p.Lys158del
NP_064716.2:p.Lys158del
NC_000006.11:g.88255395_88255397del
NC_000006.11:g.88255395_88255397delTTT
NM_020320.3:c.472_474del
NM_020320.3:c.472_474delAAA
NM_020320.4:c.472_474delAAA
NM_020320.5:c.472_474delAAAMANE SELECT
NR_134857.2:n.502_504del
NR_146738.2:n.723_725del
NR_146740.2:n.723_725del
NR_146742.2:n.885_887del
NR_146743.2:n.723_725del
NR_146744.2:n.723_725del
NR_146746.2:n.941_943del
NR_146748.2:n.723_725del
NR_146749.2:n.723_725del
NR_146750.2:n.723_725del
NR_146751.2:n.723_725del
NR_146752.2:n.667_669del
NR_146755.2:n.723_725del
NR_146756.2:n.502_504del
NR_146757.2:n.649_651del

Protein change:

K158del

Links:

dbSNP: rs757743894

NCBI 1000 Genomes Browser:

rs757743894

Molecular consequence:

NM_001318785.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350506.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350507.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350508.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350509.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350510.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350511.2:c.-54_-52del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001350505.2:c.472_474del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_020320.5:c.472_474del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_134857.2:n.502_504del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146738.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146740.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146742.2:n.885_887del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146743.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146744.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146746.2:n.941_943del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146748.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146749.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146750.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146751.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146752.2:n.667_669del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146755.2:n.723_725del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146756.2:n.502_504del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146757.2:n.649_651del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Pontocerebellar hypoplasia type 6 (PCH6)
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
SCV000992716	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 28, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003813880	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 13, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005674064	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 9, 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

SCV000992716

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 28, 2024)

unknown

clinical testing

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

SCV003813880

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 13, 2023)

germline

clinical testing

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

SCV005674064

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 9, 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	unknown	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 Baylor Genetics, SCV000992716.3

#	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 Revvity Omics, Revvity, SCV003813880.2

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV005674064.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 16, 2025

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