NM_001611.5(ACP5):c.383A>G (p.Lys128Arg) AND Spondyloenchondrodysplasia with immune dysregulation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 16, 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:: RCV001878542.6

Allele description [Variation Report for NM_001611.5(ACP5):c.383A>G (p.Lys128Arg)]

NM_001611.5(ACP5):c.383A>G (p.Lys128Arg)

Gene:

ACP5:acid phosphatase 5, tartrate resistant [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_001611.5(ACP5):c.383A>G (p.Lys128Arg)

HGVS:

NC_000019.10:g.11576722T>C
NG_028127.1:g.7265A>G
NM_001111034.3:c.383A>G
NM_001111035.3:c.383A>G
NM_001111036.3:c.383A>G
NM_001322023.2:c.383A>G
NM_001611.5:c.383A>GMANE SELECT
NP_001104504.1:p.Lys128Arg
NP_001104505.1:p.Lys128Arg
NP_001104506.1:p.Lys128Arg
NP_001308952.1:p.Lys128Arg
NP_001602.1:p.Lys128Arg
LRG_1218t1:c.383A>G
LRG_1218:g.7265A>G
LRG_1218p1:p.Lys128Arg
NC_000019.9:g.11687537T>C

Protein change:

K128R

Links:

dbSNP: rs750563102

NCBI 1000 Genomes Browser:

rs750563102

Molecular consequence:

NM_001111034.3:c.383A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001111035.3:c.383A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001111036.3:c.383A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322023.2:c.383A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001611.5:c.383A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Spondyloenchondrodysplasia with immune dysregulation (SPENCDI)
Synonyms:: COMBINED IMMUNODEFICIENCY WITH AUTOIMMUNITY AND SPONDYLOMETAPHYSEAL DYSPLASIA; ROIFMAN IMMUNOSKELETAL SYNDROME; SPONDYLOENCHONDRODYSPLASIA WITH OR WITHOUT IMMUNE DYSREGULATION
Identifiers:: MONDO: MONDO:0011939; MedGen: C1842763; OMIM: 607944

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002126064	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 16, 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

SCV002126064

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 16, 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, SCV002126064.3

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

Description

This sequence change replaces lysine with arginine at codon 128 of the ACP5 protein (p.Lys128Arg). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and arginine. 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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals affected with ACP5-related conditions. This variant is present in population databases (rs750563102, ExAC 0.001%).

#	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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