NM_001038603.3(MARVELD2):c.1407C>T (p.Tyr469=) AND not specified

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Aug 24, 2020
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:: RCV000036811.13

Allele description [Variation Report for NM_001038603.3(MARVELD2):c.1407C>T (p.Tyr469=)]

NM_001038603.3(MARVELD2):c.1407C>T (p.Tyr469=)

Gene:

MARVELD2:MARVEL domain containing 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q13.2

Genomic location:

Preferred name:

NM_001038603.3(MARVELD2):c.1407C>T (p.Tyr469=)

HGVS:

NC_000005.10:g.69432997C>T
NG_017201.2:g.22886C>T
NM_001038603.3:c.1407C>TMANE SELECT
NM_001244734.2:c.1371C>T
NP_001033692.2:p.Tyr469=
NP_001231663.1:p.Tyr457=
LRG_1380t1:c.1407C>T
LRG_1380:g.22886C>T
LRG_1380p1:p.Tyr469=
NC_000005.9:g.68728824C>T
NG_017201.1:g.22886C>T
NM_001038603.2:c.1407C>T
c.1407C>T
p.Tyr469Tyr

Links:

dbSNP: rs61736168

NCBI 1000 Genomes Browser:

rs61736168

Molecular consequence:

NM_001038603.3:c.1407C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001244734.2:c.1371C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000060466	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Sep 3, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001476674	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics criteria)	Benign (Aug 24, 2020)	unknown	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

SCV000060466

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Sep 3, 2015)

germline

clinical testing

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

SCV001476674

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics criteria)

Benign
(Aug 24, 2020)

unknown

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	not provided	5	5	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000060466.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	PubMed (1)

Description

p.Tyr469Tyr in Exon 5 of MARVELD2: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wi thin the splice consensus sequence, and has been identified in 0.2% (107/66738) by the Exome Aggregation Consortium (http://exac.broadinstitute.org/; dbSNP rs61 736168).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		5	not provided	5	not provided

From Athena Diagnostics, SCV001476674.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 7, 2024

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