NM_003172.4(SURF1):c.836A>T (p.Tyr279Phe) AND Leigh syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 20, 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:: RCV001908561.2

Allele description

NM_003172.4(SURF1):c.836A>T (p.Tyr279Phe)

Gene:

SURF1:SURF1 cytochrome c oxidase assembly factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.2

Genomic location:

Preferred name:

NM_003172.4(SURF1):c.836A>T (p.Tyr279Phe)

HGVS:

NC_000009.12:g.133351980T>A
NG_008477.1:g.9527A>T
NM_001280787.1:c.509A>T
NM_003172.4:c.836A>TMANE SELECT
NP_001267716.1:p.Tyr170Phe
NP_003163.1:p.Tyr279Phe
NC_000009.11:g.136218835T>A

Protein change:

Y170F

Links:

dbSNP: rs587758543

NCBI 1000 Genomes Browser:

rs587758543

Molecular consequence:

NM_001280787.1:c.509A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003172.4:c.836A>T - missense variant - [Sequence Ontology: SO:0001583]

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: C0023264; Orphanet: 506; OMIM: 256000

Recent activity

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RecName: Full=tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial; Alt...
RecName: Full=tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial; AltName: Full=N6-L-threonylcarbamoyladenine synthase; Short=t(6)A synthase; AltName: Full=O-sialoglycoprotein endopeptidase-like protein 1; AltName: Full=t(6)A37 threonylcarbamoyladenosine biosynthesis protein Osgepl1; AltName: Full=tRNA threonylcarbamoyladenosine biosynthesis protein Osgepl1; Flags: Precursor
gi|160013230|sp|Q6PEB4.2|OSGL1_MOUS

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002163154	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 20, 2021)	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

SCV002163154

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 20, 2021)

germline

clinical testing

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

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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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002163154.2

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

Description

This sequence change replaces tyrosine with phenylalanine at codon 279 of the SURF1 protein (p.Tyr279Phe). The tyrosine residue is moderately conserved and there is a small physicochemical difference between tyrosine and phenylalanine. This variant is present in population databases (rs587758543, ExAC 0.009%). This variant has not been reported in the literature in individuals affected with SURF1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 19, 2024

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