NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser) AND Glaucoma 3A

Germline classification:: Benign (2 submissions)
Last evaluated:: Jul 30, 2021
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:: RCV000370643.15

Allele description [Variation Report for NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser)]

NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser)

Gene:

CYP1B1:cytochrome P450 family 1 subfamily B member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p22.2

Genomic location:

Preferred name:

NM_000104.4(CYP1B1):c.355G>T (p.Ala119Ser)

HGVS:

NC_000002.12:g.38075034C>A
NG_008386.2:g.6068G>T
NM_000104.4:c.355G>TMANE SELECT
NP_000095.2:p.Ala119Ser
NP_000095.2:p.Ala119Ser
NP_000095.2:p.Ala119Ser
NC_000002.11:g.38302177C>A
NM_000104.3:c.355G>T
Q16678:p.Ala119Ser

Protein change:

A119S

Links:

UniProtKB: Q16678#VAR_011753; dbSNP: rs1056827

NCBI 1000 Genomes Browser:

rs1056827

Molecular consequence:

NM_000104.4:c.355G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glaucoma 3A
Synonyms:: Glaucoma 3, primary congenital, A
Identifiers:: MONDO: MONDO:0009277; MedGen: C1856439; Orphanet: 98976; Orphanet: 98977; OMIM: 231300

Recent activity

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netrin-G1 isoform X3 [Ovis aries]
netrin-G1 isoform X3 [Ovis aries]
gi|2062748081|ref|XP_042107584.1|

Protein
PREDICTED: Homo sapiens abraxas 2, BRISC complex subunit (ABRAXAS2), transcript ...
PREDICTED: Homo sapiens abraxas 2, BRISC complex subunit (ABRAXAS2), transcript variant X2, mRNA
gi|2462518065|ref|XM_054365318.1|

Nucleotide
Sporothrix schenckii 1099-18 catalase (SPSK_06226), partial mRNA
Sporothrix schenckii 1099-18 catalase (SPSK_06226), partial mRNA
gi|1026947008|ref|XM_016732933.1|

Nucleotide
Homo sapiens GLI family zinc finger 2 (GLI2), transcript variant 1, mRNA
Homo sapiens GLI family zinc finger 2 (GLI2), transcript variant 1, mRNA
gi|1698389211|ref|NM_001371271.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000430284	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10739169, 16384942 Citation Link,
SCV001876487	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 30, 2021)	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

SCV000430284

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV001876487

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 30, 2021)

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Association of CYP1B1 genetic polymorphism with incidence to breast and lung cancer.

Watanabe J, Shimada T, Gillam EM, Ikuta T, Suemasu K, Higashi Y, Gotoh O, Kawajiri K.

Pharmacogenetics. 2000 Feb;10(1):25-33.

PubMed [citation]

PMID:: 10739169

Globally, CYP1B1 mutations in primary congenital glaucoma are strongly structured by geographic and haplotype backgrounds.

Chakrabarti S, Kaur K, Kaur I, Mandal AK, Parikh RS, Thomas R, Majumder PP.

Invest Ophthalmol Vis Sci. 2006 Jan;47(1):43-7.

PubMed [citation]

PMID:: 16384942

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000430284.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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 Genome-Nilou Lab, SCV001876487.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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