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:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens RAB, member of RAS oncogene family like 2A (RABL2A), tra...
PREDICTED: Homo sapiens RAB, member of RAS oncogene family like 2A (RABL2A), transcript variant X18, mRNA
gi|2462569574|ref|XM_054340277.1|

Nucleotide
mRNA-capping enzyme isoform b [Homo sapiens]
mRNA-capping enzyme isoform b [Homo sapiens]
gi|556695469|ref|NP_001273355.1|

Protein
hypothetical protein MPH_05288 [Macrophomina phaseolina MS6]
hypothetical protein MPH_05288 [Macrophomina phaseolina MS6]
gi|407924430|gb|EKG17480.1||gnl|WGS |MPH_05288

Protein
RecName: Full=Glutamate-1-semialdehyde 2,1-aminomutase; Short=GSA; AltName: Full...
RecName: Full=Glutamate-1-semialdehyde 2,1-aminomutase; Short=GSA; AltName: Full=Glutamate-1-semialdehyde aminotransferase; Short=GSA-AT
gi|254799628|sp|B8G822.1|GSA_CHLAD

Protein
type I restriction enzyme, S subunit [Halopseudomonas pachastrellae]
type I restriction enzyme, S subunit [Halopseudomonas pachastrellae]
gi|1097646021|emb|SFN01576.1||gnl|W UD|SFN01576

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000857565	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Uncertain significance (Aug 30, 2018)	germline	clinical testing	Citation Link,
SCV001715285	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 18, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002290432	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 31, 2022)	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

SCV000857565

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Uncertain significance
(Aug 30, 2018)

germline

clinical testing

Citation Link,

SCV001715285

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 18, 2021)

germline

clinical testing

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

SCV002290432

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 31, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	4	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

#	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		4	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001715285.2

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

#	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

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

#	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 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.

#	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: Sep 29, 2024

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