NM_001377.3(DYNC2H1):c.5473A>G (p.Ile1825Val) AND Asphyxiating thoracic dystrophy 3

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 25, 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:: RCV001285728.8

Allele description [Variation Report for NM_001377.3(DYNC2H1):c.5473A>G (p.Ile1825Val)]

NM_001377.3(DYNC2H1):c.5473A>G (p.Ile1825Val)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_001377.3(DYNC2H1):c.5473A>G (p.Ile1825Val)

HGVS:

NC_000011.10:g.103173220A>G
NG_016423.2:g.68790A>G
NM_001080463.2:c.5473A>G
NM_001377.3:c.5473A>GMANE SELECT
NP_001073932.1:p.Ile1825Val
NP_001368.2:p.Ile1825Val
NC_000011.9:g.103043949A>G
NG_016423.1:g.68790A>G
NM_001080463.1:c.5473A>G

Protein change:

I1825V

Links:

dbSNP: rs201860217

NCBI 1000 Genomes Browser:

rs201860217

Molecular consequence:

NM_001080463.2:c.5473A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001377.3:c.5473A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001472207	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Uncertain significance (Oct 30, 2019)	germline	clinical testing	Citation Link,
SCV003835354	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 25, 2022)	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

SCV001472207

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Uncertain significance
(Oct 30, 2019)

germline

clinical testing

Citation Link,

SCV003835354

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 25, 2022)

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001472207.1

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

Description

The DYNC2H1 c.5473A>G; p.Ile1825Val variant (rs201860217), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 283519). This variant is found in the general population with an overall allele frequency of 0.02% (55/270634 alleles) in the Genome Aggregation Database. The isoleucine at codon 1825 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Due to limited information, the clinical significance of the p.Ile1825Val variant is uncertain at this time.

#	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 Baylor Genetics, SCV003835354.1

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine