NM_001202.6(BMP4):c.673A>G (p.Thr225Ala) AND Microphthalmia with brain and digit anomalies

Germline classification:: Benign (1 submission)
Last evaluated:: Aug 7, 2017
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:: RCV001112674.4

Allele description [Variation Report for NM_001202.6(BMP4):c.673A>G (p.Thr225Ala)]

NM_001202.6(BMP4):c.673A>G (p.Thr225Ala)

Gene:

BMP4:bone morphogenetic protein 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q22.2

Genomic location:

Preferred name:

NM_001202.6(BMP4):c.673A>G (p.Thr225Ala)

HGVS:

NC_000014.9:g.53950586T>C
NG_009215.1:g.11251A>G
NM_001202.6:c.673A>GMANE SELECT
NM_001347912.1:c.814A>G
NM_001347913.2:c.484A>G
NM_001347914.2:c.673A>G
NM_001347915.2:c.484A>G
NM_001347916.1:c.673A>G
NM_001347917.1:c.484A>G
NM_130850.5:c.673A>G
NM_130851.4:c.673A>G
NP_001193.2:p.Thr225Ala
NP_001334841.1:p.Thr272Ala
NP_001334842.1:p.Thr162Ala
NP_001334843.1:p.Thr225Ala
NP_001334844.1:p.Thr162Ala
NP_001334845.1:p.Thr225Ala
NP_001334846.1:p.Thr162Ala
NP_570911.2:p.Thr225Ala
NP_570912.2:p.Thr225Ala
NC_000014.8:g.54417304T>C
NC_000014.8:g.54417304T>C
NM_001202.3:c.673A>G

Protein change:

T162A

Links:

dbSNP: rs144556455

NCBI 1000 Genomes Browser:

rs144556455

Molecular consequence:

NM_001202.6:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347912.1:c.814A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347913.2:c.484A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347914.2:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347915.2:c.484A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347916.1:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001347917.1:c.484A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130850.5:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_130851.4:c.673A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Microphthalmia with brain and digit anomalies (MCOPS6)
Synonyms:: Microphthalmia syndromic 6; Microphthalmia and pituitary anomalies; Microphthalmia with brain and digit developmental anomalies; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011936; MedGen: C1864689; Orphanet: 139471; OMIM: 607932

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001270359	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Aug 7, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12404109, 20949628 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001270359

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Aug 7, 2017)

germline

clinical testing

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

Citation Link

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

Evaluation of BMP4 and its specific inhibitor NOG as candidates in human neural tube defects (NTDs).

Felder B, Stegmann K, Schultealbert A, Geller F, Strehl E, Ermert A, Koch MC.

Eur J Hum Genet. 2002 Nov;10(11):753-6.

PubMed [citation]

PMID:: 12404109

Evaluation of germline BMP4 mutation as a cause of colorectal cancer.

Lubbe SJ, Pittman AM, Matijssen C, Twiss P, Olver B, Lloyd A, Qureshi M, Brown N, Nye E, Stamp G, Blagg J, Houlston RS.

Hum Mutat. 2011 Jan;32(1):E1928-38. doi: 10.1002/humu.21376. Epub 2010 Oct 14.

PubMed [citation]

PMID:: 20949628
PMCID:: PMC3034195

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001270359.1

#	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

Last Updated: Oct 20, 2024

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