NM_000103.4(CYP19A1):c.628G>A (p.Glu210Lys) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 14, 2023
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:: RCV001851942.3

Allele description [Variation Report for NM_000103.4(CYP19A1):c.628G>A (p.Glu210Lys)]

NM_000103.4(CYP19A1):c.628G>A (p.Glu210Lys)

Genes:

MIR4713HG:MIR4713 host gene [Gene - HGNC]
CYP19A1:cytochrome P450 family 19 subfamily A member 1 [Gene - OMIM - HGNC]
PIRC66:piwi-interacting RNA cluster 66 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q21.2

Genomic location:

Preferred name:

NM_000103.4(CYP19A1):c.628G>A (p.Glu210Lys)

HGVS:

NC_000015.10:g.51222349C>T
NG_007982.1:g.121250G>A
NM_000103.4:c.628G>AMANE SELECT
NM_001347248.1:c.628G>A
NM_001347249.2:c.628G>A
NM_001347250.2:c.628G>A
NM_001347251.2:c.628G>A
NM_001347252.2:c.628G>A
NM_001347253.2:c.628G>A
NM_001347254.2:c.628G>A
NM_001347255.2:c.628G>A
NM_001347256.2:c.628G>A
NM_031226.3:c.628G>A
NP_000094.2:p.Glu210Lys
NP_001334177.1:p.Glu210Lys
NP_001334178.1:p.Glu210Lys
NP_001334179.1:p.Glu210Lys
NP_001334180.1:p.Glu210Lys
NP_001334181.1:p.Glu210Lys
NP_001334182.1:p.Glu210Lys
NP_001334183.1:p.Glu210Lys
NP_001334184.1:p.Glu210Lys
NP_001334185.1:p.Glu210Lys
NP_112503.1:p.Glu210Lys
NC_000015.9:g.51514546C>T

Protein change:

E210K; GLU210LYS

Links:

OMIM: 107910.0012; dbSNP: rs121434538

NCBI 1000 Genomes Browser:

rs121434538

Molecular consequence:

NM_000103.4:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347248.1:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347249.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347250.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347251.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347252.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347253.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347254.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347255.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347256.2:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_031226.3:c.628G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002237841	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 14, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 17576681, 9536098, 14602738, 25301327, 25415177, 27693882, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002237841

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 14, 2023)

germline

clinical testing

PubMed (7)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (7)

Details of each submission

From Invitae, SCV002237841.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 17826). This variant is also known as c.655G>A. This missense change has been observed in individuals with CYP19A1-related conditions (PMID: 14602738, 25301327, 25415177, 27693882). This variant is present in population databases (rs121434538, gnomAD 0.006%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 210 of the CYP19A1 protein (p.Glu210Lys). This variant also falls at the last nucleotide of exon 6, which is part of the consensus splice site for this exon.

#	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: Feb 20, 2024

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