U.S. flag

An official website of the United States government

NM_002979.5(SCP2):c.1234A>G (p.Ser412Gly) AND not provided

Germline classification:
Uncertain significance (3 submissions)
Last evaluated:
Oct 31, 2022
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:
RCV000729872.12

Allele description [Variation Report for NM_002979.5(SCP2):c.1234A>G (p.Ser412Gly)]

NM_002979.5(SCP2):c.1234A>G (p.Ser412Gly)

Gene:
SCP2:sterol carrier protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p32.3
Genomic location:
Preferred name:
NM_002979.5(SCP2):c.1234A>G (p.Ser412Gly)
HGVS:
  • NC_000001.11:g.53015042A>G
  • NG_012211.1:g.92767A>G
  • NM_001007099.3:c.22A>G
  • NM_001007100.3:c.22A>G
  • NM_001007250.3:c.22A>G
  • NM_001193599.2:c.1162A>G
  • NM_001193600.2:c.1102A>G
  • NM_001193617.2:c.991A>G
  • NM_002979.5:c.1234A>GMANE SELECT
  • NP_001007100.1:p.Ser8Gly
  • NP_001007101.1:p.Arg8Gly
  • NP_001007251.1:p.Ser8Gly
  • NP_001180528.1:p.Ser388Gly
  • NP_001180529.1:p.Ser368Gly
  • NP_001180546.1:p.Ser331Gly
  • NP_002970.2:p.Ser412Gly
  • NC_000001.10:g.53480714A>G
  • NM_002979.4:c.1234A>G
  • p.Ser412Gly
Protein change:
R8G
Links:
dbSNP: rs201094447
NCBI 1000 Genomes Browser:
rs201094447
Molecular consequence:
  • NM_001007099.3:c.22A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007100.3:c.22A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001007250.3:c.22A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001193599.2:c.1162A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001193600.2:c.1102A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001193617.2:c.991A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002979.5:c.1234A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
4

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000857565Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)
Uncertain significance
(Aug 30, 2018)
germlineclinical testing

Citation Link,

SCV001715285Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Aug 18, 2021)
germlineclinical testing

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

SCV002290432Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Oct 31, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown4not providednot providednot providednot 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

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 Eurofins Ntd Llc (ga), SCV000857565.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided4not providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001715285.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002290432.2

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

Description

This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 412 of the SCP2 protein (p.Ser412Gly). This variant is present in population databases (rs201094447, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with SCP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 594561). 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.

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

Last Updated: Sep 29, 2024