NM_001377.3(DYNC2H1):c.8885AAG[1] (p.Glu2963del) AND Asphyxiating thoracic dystrophy 3

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 1, 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:: RCV000988632.2

Allele description [Variation Report for NM_001377.3(DYNC2H1):c.8885AAG[1] (p.Glu2963del)]

NM_001377.3(DYNC2H1):c.8885AAG[1] (p.Glu2963del)

Gene:

DYNC2H1:dynein cytoplasmic 2 heavy chain 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_001377.3(DYNC2H1):c.8885AAG[1] (p.Glu2963del)

HGVS:

NC_000011.10:g.103219967AAG[1]
NC_000011.10:g.103219967_103219969AAG[1]
NG_016423.2:g.115537AAG[1]
NM_001080463.1:c.8888_8890del
NM_001080463.2:c.8885AAG[1]
NM_001377.3:c.8885AAG[1]MANE SELECT
NP_001073932.1:p.Glu2963del
NP_001368.2:p.Glu2963del
NC_000011.9:g.103090694_103090696delAGA
NC_000011.9:g.103090696AAG[1]
NM_001377.3:c.8888_8890delMANE SELECT

Protein change:

E2963del

Links:

dbSNP: rs770387587

NCBI 1000 Genomes Browser:

rs770387587

Molecular consequence:

NM_001080463.2:c.8885AAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001377.3:c.8885AAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

Name:: Asphyxiating thoracic dystrophy 3
Synonyms:: POLYDACTYLY WITH NEONATAL CHONDRODYSTROPHY, TYPE I; SHORT-RIB THORACIC DYSPLASIA 3/6 WITH POLYDACTYLY, DIGENIC; Short rib polydactyly syndrome 2B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013127; MedGen: C0036069; Orphanet: 474; Orphanet: 93269; Orphanet: 93271; OMIM: 613091

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001138417	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Uncertain significance (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV002572769	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 1, 2022)	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

SCV001138417

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Uncertain significance
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV002572769

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 1, 2022)

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	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 Mendelics, SCV001138417.1

#	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

From 3billion, SCV002572769.1

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

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). This variant leads to inframe deletion located in a nonrepeat region and it is predicted to change the length of the protein and disrupt normal protein function. Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Jul 29, 2023

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