NM_004006.3(DMD):c.10097_10099del (p.Gly3366del) AND Duchenne muscular dystrophy

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 9, 2022
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:: RCV000465638.11

Allele description [Variation Report for NM_004006.3(DMD):c.10097_10099del (p.Gly3366del)]

NM_004006.3(DMD):c.10097_10099del (p.Gly3366del)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp21.2

Genomic location:

Preferred name:

NM_004006.3(DMD):c.10097_10099del (p.Gly3366del)

HGVS:

NC_000023.10:g.31196910_31196912del
NC_000023.11:g.31178795_31178797del
NG_012232.1:g.2165815_2165817del
NM_000109.4:c.10073_10075del
NM_004006.3:c.10097_10099delMANE SELECT
NM_004009.3:c.10085_10087del
NM_004010.3:c.9728_9730del
NM_004011.4:c.6074_6076del
NM_004012.4:c.6065_6067del
NM_004013.3:c.2717_2719del
NM_004014.3:c.1910_1912del
NM_004015.3:c.893_895del
NM_004016.3:c.893_895del
NM_004017.3:c.893_895del
NM_004018.3:c.893_895del
NM_004019.3:c.893_895del
NM_004020.4:c.2717_2719del
NM_004021.3:c.2717_2719del
NM_004022.3:c.2717_2719del
NM_004023.3:c.2717_2719del
NP_000100.3:p.Gly3358del
NP_003997.2:p.Gly3366del
NP_004000.1:p.Gly3362del
NP_004001.1:p.Gly3243del
NP_004002.3:p.Gly2025del
NP_004003.2:p.Gly2022del
NP_004004.2:p.Gly906del
NP_004005.2:p.Gly637del
NP_004006.1:p.Gly298del
NP_004007.1:p.Gly298del
NP_004008.1:p.Gly298del
NP_004009.1:p.Gly298del
NP_004010.1:p.Gly298del
NP_004011.3:p.Gly906del
NP_004012.2:p.Gly906del
NP_004013.2:p.Gly906del
NP_004014.2:p.Gly906del
LRG_199:g.2165815_2165817del
NC_000023.10:g.31196910_31196912del
NC_000023.10:g.31196910_31196912delCTC
NC_000023.10:g.31196912_31196914del
NM_004006.2:c.10097_10099delGAG

Protein change:

G2022del

Links:

dbSNP: rs1060502613

NCBI 1000 Genomes Browser:

rs1060502613

Molecular consequence:

NM_000109.4:c.10073_10075del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004006.3:c.10097_10099del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004009.3:c.10085_10087del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004010.3:c.9728_9730del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004011.4:c.6074_6076del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004012.4:c.6065_6067del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004013.3:c.2717_2719del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004014.3:c.1910_1912del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004015.3:c.893_895del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004016.3:c.893_895del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004017.3:c.893_895del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004018.3:c.893_895del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004019.3:c.893_895del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004020.4:c.2717_2719del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004021.3:c.2717_2719del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004022.3:c.2717_2719del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004023.3:c.2717_2719del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Duchenne muscular dystrophy (DMD)
Synonyms:: Muscular dystrophy, pseudohypertrophic progressive, Duchenne type
Identifiers:: MONDO: MONDO:0010679; MedGen: C0013264; Orphanet: 98896; OMIM: 310200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000550250	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 9, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19937601, 28859693, 28492532
SCV001141578	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Uncertain significance (May 28, 2019)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000550250

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 9, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV001141578

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Uncertain significance
(May 28, 2019)

unknown

clinical testing

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

Citations

PubMed

Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort.

Flanigan KM, Dunn DM, von Niederhausern A, Soltanzadeh P, Gappmaier E, Howard MT, Sampson JB, Mendell JR, Wall C, King WM, Pestronk A, Florence JM, Connolly AM, Mathews KD, Stephan CM, Laubenthal KS, Wong BL, Morehart PJ, Meyer A, Finkel RS, Bonnemann CG, Medne L, et al.

Hum Mutat. 2009 Dec;30(12):1657-66. doi: 10.1002/humu.21114.

PubMed [citation]

PMID:: 19937601
PMCID:: PMC3404892

Comprehensive analysis for genetic diagnosis of Dystrophinopathies in Japan.

Okubo M, Goto K, Komaki H, Nakamura H, Mori-Yoshimura M, Hayashi YK, Mitsuhashi S, Noguchi S, Kimura E, Nishino I.

Orphanet J Rare Dis. 2017 Aug 31;12(1):149. doi: 10.1186/s13023-017-0703-4.

PubMed [citation]

PMID:: 28859693
PMCID:: PMC5580216

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000550250.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant, c.10097_10099del, results in the deletion of 1 amino acid(s) of the DMD protein (p.Gly3366del), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 409880). This variant has been observed in individuals with Duchenne Muscular Dystrophy or DMD (PMID: 19937601, 28859693). This variant is not present in population databases (gnomAD no frequency).

#	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 Mendelics, SCV001141578.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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: Mar 16, 2024

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