NM_001625.4(AK2):c.638C>A (p.Ser213Tyr) AND Reticular dysgenesis

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 20, 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:: RCV000798556.7

Allele description [Variation Report for NM_001625.4(AK2):c.638C>A (p.Ser213Tyr)]

NM_001625.4(AK2):c.638C>A (p.Ser213Tyr)

Gene:

AK2:adenylate kinase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p35.1

Genomic location:

Preferred name:

NM_001625.4(AK2):c.638C>A (p.Ser213Tyr)

HGVS:

NC_000001.11:g.33013263G>T
NG_016269.1:g.28629C>A
NM_001199199.3:c.614C>A
NM_001319139.3:c.494C>A
NM_001319140.2:c.494C>A
NM_001319141.3:c.638C>A
NM_001319142.3:c.512C>A
NM_001319143.2:c.*141C>A
NM_001625.4:c.638C>AMANE SELECT
NM_013411.5:c.638C>A
NP_001186128.1:p.Ser205Tyr
NP_001306068.1:p.Ser165Tyr
NP_001306069.1:p.Ser165Tyr
NP_001306070.1:p.Ser213Tyr
NP_001306071.1:p.Ser171Tyr
NP_001616.1:p.Ser213Tyr
NP_037543.1:p.Ser213Tyr
LRG_133:g.28629C>A
NC_000001.10:g.33478864G>T
NM_001625.3:c.638C>A
NR_134976.3:n.598C>A

Protein change:

S165Y

Links:

dbSNP: rs139238739

NCBI 1000 Genomes Browser:

rs139238739

Molecular consequence:

NM_001319143.2:c.*141C>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001199199.3:c.614C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001319139.3:c.494C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001319140.2:c.494C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001319141.3:c.638C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001319142.3:c.512C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001625.4:c.638C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_013411.5:c.638C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_134976.3:n.598C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Reticular dysgenesis
Synonyms:: ALEUKOCYTOSIS; HEMATOPOIETIC HYPOPLASIA, GENERALIZED; RETICULAR DYSGENESIA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009973; MedGen: C0272167; Orphanet: 33355; OMIM: 267500

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000938177	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 20, 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

SCV000938177

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 20, 2021)

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	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000938177.4

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

Description

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. 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: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with AK2-related disease. This variant is present in population databases (rs139238739, ExAC 0.003%). This sequence change replaces serine with tyrosine at codon 213 of the AK2 protein (p.Ser213Tyr). The serine residue is moderately conserved and there is a large physicochemical difference between serine and tyrosine.

#	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: Sep 29, 2024

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