NM_001770.6(CD19):c.1121C>G (p.Thr374Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 28, 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:: RCV002932883.2

Allele description [Variation Report for NM_001770.6(CD19):c.1121C>G (p.Thr374Ser)]

NM_001770.6(CD19):c.1121C>G (p.Thr374Ser)

Gene:

CD19:CD19 molecule [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p11.2

Genomic location:

Preferred name:

NM_001770.6(CD19):c.1121C>G (p.Thr374Ser)

HGVS:

NC_000016.10:g.28937059C>G
NG_007275.1:g.10121C>G
NM_001178098.2:c.1121C>G
NM_001385732.1:c.854C>G
NM_001770.6:c.1121C>GMANE SELECT
NP_001171569.1:p.Thr374Ser
NP_001372661.1:p.Thr285Ser
NP_001761.3:p.Thr374Ser
NP_001761.3:p.Thr374Ser
LRG_35t1:c.1121C>G
LRG_35:g.10121C>G
LRG_35p1:p.Thr374Ser
NC_000016.9:g.28948380C>G
NM_001770.5:c.1121C>G
NR_169755.1:n.1463C>G

Protein change:

T285S

Molecular consequence:

NM_001178098.2:c.1121C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001385732.1:c.854C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001770.6:c.1121C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_169755.1:n.1463C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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T-complex protein 10A homolog 2 [Rattus norvegicus]
T-complex protein 10A homolog 2 [Rattus norvegicus]
gi|2316633505|ref|NP_001399567.1|

Protein
Taxonomy Links for GEO Profiles (Select 104565021) (1)
Taxonomy
Phocaeicola vulgatus strain AM13-21 AM13-21.Scaf1, whole genome shotgun sequence
Phocaeicola vulgatus strain AM13-21 AM13-21.Scaf1, whole genome shotgun sequence
gi|1473861755|ref|NZ_QRLF01000001.1 |WGS:NZ_QRLF01|AM13-21.Scaf1

Nucleotide
Taxonomy Links for GEO Profiles (Select 12580272) (1)
Taxonomy

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003263847	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 28, 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

SCV003263847

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 28, 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	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003263847.1

#	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 threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 374 of the CD19 protein (p.Thr374Ser). This variant is present in population databases (no rsID available, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CD19-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: Sep 29, 2024

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