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NM_003172.4(SURF1):c.595_598del (p.Gly199fs) AND Leigh syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 2, 2021
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:
RCV001775299.1

Allele description [Variation Report for NM_003172.4(SURF1):c.595_598del (p.Gly199fs)]

NM_003172.4(SURF1):c.595_598del (p.Gly199fs)

Gene:
SURF1:SURF1 cytochrome c oxidase assembly factor [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.2
Genomic location:
Preferred name:
NM_003172.4(SURF1):c.595_598del (p.Gly199fs)
HGVS:
  • NC_000009.12:g.133352602_133352605del
  • NG_008477.1:g.8905_8908del
  • NM_001280787.1:c.268_271del
  • NM_003172.4:c.595_598delMANE SELECT
  • NP_001267716.1:p.Gly90fs
  • NP_003163.1:p.Gly199fs
  • NC_000009.11:g.136219457_136219460del
  • NM_003172.3:c.595_598del
Protein change:
G199fs
Links:
dbSNP: rs2119081217
NCBI 1000 Genomes Browser:
rs2119081217
Molecular consequence:
  • NM_001280787.1:c.268_271del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003172.4:c.595_598del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Leigh syndrome (NULS)
Synonyms:
Leigh Disease; Subacute necrotizing encephalopathy; Necrotizing encephalopathy infantile subacute of Leigh; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009723; MedGen: C2931891; Orphanet: 506; OMIM: 256000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0020120573billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 2, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot provided1not providedclinical 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 3billion, SCV002012057.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is not observed in the gnomAD v2.1.1 dataset (PM2). Patient's phenotype is considered compatible with Leigh syndrome, due to COX IV deficiency (3billion dataset, PP4). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

Last Updated: Nov 24, 2024