NM_004946.3(DOCK2):c.215A>T (p.Glu72Val) AND DOCK2 deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 29, 2021
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:: RCV001306879.6

Allele description

NM_004946.3(DOCK2):c.215A>T (p.Glu72Val)

Gene:

DOCK2:dedicator of cytokinesis 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.1

Genomic location:

Preferred name:

NM_004946.3(DOCK2):c.215A>T (p.Glu72Val)

HGVS:

NC_000005.10:g.169670588A>T
NG_051800.1:g.38342A>T
NM_004946.3:c.215A>TMANE SELECT
NP_004937.1:p.Glu72Val
LRG_1227t1:c.215A>T
LRG_1227:g.38342A>T
LRG_1227p1:p.Glu72Val
NC_000005.9:g.169097592A>T
NR_156756.1:n.267A>T

Protein change:

E72V

Links:

dbSNP: rs1375534866

NCBI 1000 Genomes Browser:

rs1375534866

Molecular consequence:

NM_004946.3:c.215A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_156756.1:n.267A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: DOCK2 deficiency
Synonyms:: Immunodeficiency 40
Identifiers:: MONDO: MONDO:0014637; MedGen: C4225328; Orphanet: 447737; OMIM: 616433

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Alvinella pompejana symbiont apg68 16S ribosomal RNA gene, partial sequence
Alvinella pompejana symbiont apg68 16S ribosomal RNA gene, partial sequence
gi|5901778|gb|AF180305.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001496265	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 29, 2021)	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

SCV001496265

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 29, 2021)

germline

clinical testing

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

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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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001496265.4

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with DOCK2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with valine at codon 72 of the DOCK2 protein (p.Glu72Val). The glutamic acid residue is weakly conserved and there is a moderate physicochemical difference between glutamic acid and valine. 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.

#	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

Last Updated: Feb 28, 2024

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