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NM_003172.4(SURF1):c.563A>G (p.Asn188Ser) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 25, 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:
RCV002222439.1

Allele description [Variation Report for NM_003172.4(SURF1):c.563A>G (p.Asn188Ser)]

NM_003172.4(SURF1):c.563A>G (p.Asn188Ser)

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.563A>G (p.Asn188Ser)
HGVS:
  • NC_000009.12:g.133352719T>C
  • NG_008477.1:g.8788A>G
  • NM_001280787.1:c.236A>G
  • NM_003172.4:c.563A>GMANE SELECT
  • NP_001267716.1:p.Asn79Ser
  • NP_003163.1:p.Asn188Ser
  • NC_000009.11:g.136219574T>C
  • NM_003172.2:c.563A>G
  • NM_003172.3:c.563A>G
  • p.N188S
Protein change:
N188S
Links:
dbSNP: rs200702528
NCBI 1000 Genomes Browser:
rs200702528
Molecular consequence:
  • NM_001280787.1:c.236A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003172.4:c.563A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002500642Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Uncertain significance
(Mar 25, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

SURF1 mutations in Chinese patients with Leigh syndrome: Novel mutations, mutation spectrum, and the functional consequences.

Li Y, Wen S, Li D, Xie J, Wei X, Li X, Liu Y, Fang H, Yang Y, Lyu J.

Gene. 2018 Oct 20;674:15-24. doi: 10.1016/j.gene.2018.06.058. Epub 2018 Jun 19.

PubMed [citation]
PMID:
29933018

Outcome of Whole Exome Sequencing for Diagnostic Odyssey Cases of an Individualized Medicine Clinic: The Mayo Clinic Experience.

Lazaridis KN, Schahl KA, Cousin MA, Babovic-Vuksanovic D, Riegert-Johnson DL, Gavrilova RH, McAllister TM, Lindor NM, Abraham RS, Ackerman MJ, Pichurin PN, Deyle DR, Gavrilov DK, Hand JL, Klee EW, Stephens MC, Wick MJ, Atkinson EJ, Linden DR, Ferber MJ, Wieben ED, Farrugia G; et al.

Mayo Clin Proc. 2016 Mar;91(3):297-307. doi: 10.1016/j.mayocp.2015.12.018.

PubMed [citation]
PMID:
26944241

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002500642.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: SURF1 c.563A>G (p.Asn188Ser) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 249650 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in SURF1 causing Leigh Syndrome (0.00012 vs 0.0018), allowing no conclusion about variant significance. c.563A>G has been reported in the literature in a heterozygous individual affected with a suspected genetic disease (specific phenotype not provided) (Lazaridis_2016). This report does not provide unequivocal conclusions about association of the variant with Leigh Syndrome. Experimental evidence evaluating an impact on protein function showed that the variant decreases complex IV assembly without affecting SURF1 stability (Li_2018). This report does not allow convincing conclusions about the variant effect. A ClinVar submitter (evaluation after 2014) cites the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024