NM_003172.4(SURF1):c.589-1G>C AND Leigh syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 9, 2022
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:: RCV003058239.2

Allele description [Variation Report for NM_003172.4(SURF1):c.589-1G>C]

NM_003172.4(SURF1):c.589-1G>C

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.589-1G>C

HGVS:

NC_000009.12:g.133352609C>G
NG_008477.1:g.8898G>C
NG_008477.2:g.8878G>C
NM_001280787.1:c.262-1G>C
NM_003172.4:c.589-1G>CMANE SELECT
NC_000009.11:g.136219464C>G

Molecular consequence:

NM_001280787.1:c.262-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_003172.4:c.589-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003441318	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 9, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 11288709, 16199547, 10443880, 22488715, 24027061, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003441318

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 9, 2022)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

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

Citations

PubMed

Mutations in SURF1 are not specifically associated with Leigh syndrome.

Von Kleist-Retzow JC, Yao J, Taanman JW, Chantrel K, Chretien D, Cormier-Daire V, Rotig A, Munnich A, Rustin P, Shoubridge EA.

J Med Genet. 2001 Feb;38(2):109-13. No abstract available.

PubMed [citation]

PMID:: 11288709
PMCID:: PMC1734810

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV003441318.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Studies have shown that disruption of this splice site alters SURF1 gene expression (PMID: 11288709). This variant is also known as G603-1C. Disruption of this splice site has been observed in individual(s) with Leigh syndrome (PMID: 11288709). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 6 of the SURF1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SURF1 are known to be pathogenic (PMID: 10443880, 22488715, 24027061).

#	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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