NM_001378457.1(DMXL2):c.6247G>A (p.Ala2083Thr) AND Hearing loss, autosomal dominant 71

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 22, 2020
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:: RCV001225312.1

Allele description [Variation Report for NM_001378457.1(DMXL2):c.6247G>A (p.Ala2083Thr)]

NM_001378457.1(DMXL2):c.6247G>A (p.Ala2083Thr)

Gene:

DMXL2:Dmx like 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q21.2

Genomic location:

Preferred name:

NM_001378457.1(DMXL2):c.6247G>A (p.Ala2083Thr)

HGVS:

NC_000015.10:g.51480859C>T
NG_017155.1:g.146912G>A
NM_001174116.3:c.6247G>A
NM_001174117.3:c.4339G>A
NM_001378457.1:c.6247G>AMANE SELECT
NM_001378458.1:c.6247G>A
NM_001378459.1:c.6247G>A
NM_001378460.1:c.4228G>A
NM_001378461.1:c.6247G>A
NM_001378462.1:c.6247G>A
NM_001378463.1:c.6247G>A
NM_001378464.1:c.6007G>A
NM_015263.5:c.6247G>A
NP_001167587.1:p.Ala2083Thr
NP_001167588.1:p.Ala1447Thr
NP_001365386.1:p.Ala2083Thr
NP_001365387.1:p.Ala2083Thr
NP_001365388.1:p.Ala2083Thr
NP_001365389.1:p.Ala1410Thr
NP_001365390.1:p.Ala2083Thr
NP_001365391.1:p.Ala2083Thr
NP_001365392.1:p.Ala2083Thr
NP_001365393.1:p.Ala2003Thr
NP_056078.2:p.Ala2083Thr
NC_000015.9:g.51773056C>T
NC_000015.9:g.51773056C>T
NM_001174116.2:c.6247G>A
NR_165648.1:n.6473G>A
NR_165649.1:n.6473G>A
p.Ala2083Thr

Protein change:

A1410T

Links:

dbSNP: rs778580507

NCBI 1000 Genomes Browser:

rs778580507

Molecular consequence:

NM_001174116.3:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001174117.3:c.4339G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378457.1:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378458.1:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378459.1:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378460.1:c.4228G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378461.1:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378462.1:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378463.1:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378464.1:c.6007G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015263.5:c.6247G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_165648.1:n.6473G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165649.1:n.6473G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

Unknown function

Observations:

Condition(s)

Name:: Hearing loss, autosomal dominant 71
Synonyms:: Deafness, autosomal dominant 71
Identifiers:: MONDO: MONDO:0033258; MedGen: C4539881; OMIM: 617605

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001370541	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 22, 2020)	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

SCV001370541

Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 22, 2020)

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
Muslim	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV001370541.1

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

Description

A heterozygous missense variation in exon 24 of the DMXL2 gene that results in the amino acid substitution of Threonine for Alanine at codon 2083 was detected. The observed variant c.6247G>A (p.Ala2083Thr) has not been reported in the 1000 genomes and has a minor allele frequency of 0.007% in the ExAC database. The in silico prediction of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by SIFT, LRT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be 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	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Mar 5, 2024

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