NM_000572.3(IL10):c.507A>C (p.Glu169Asp) AND Inflammatory bowel disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 31, 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:: RCV001208795.7

Allele description [Variation Report for NM_000572.3(IL10):c.507A>C (p.Glu169Asp)]

NM_000572.3(IL10):c.507A>C (p.Glu169Asp)

Gene:

IL10:interleukin 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q32.1

Genomic location:

Preferred name:

NM_000572.3(IL10):c.507A>C (p.Glu169Asp)

HGVS:

NC_000001.11:g.206768666T>G
NG_012088.1:g.8829A>C
NM_000572.3:c.507A>CMANE SELECT
NM_001382624.1:c.252A>C
NP_000563.1:p.Glu169Asp
NP_001369553.1:p.Glu84Asp
LRG_1230t1:c.507A>C
LRG_1230:g.8829A>C
LRG_1230p1:p.Glu169Asp
NC_000001.10:g.206942011T>G
NM_000572.2:c.507A>C
NR_168466.1:n.804A>C
NR_168467.1:n.334A>C

Protein change:

E169D

Links:

dbSNP: rs568879359

NCBI 1000 Genomes Browser:

rs568879359

Molecular consequence:

NM_000572.3:c.507A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001382624.1:c.252A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_168466.1:n.804A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_168467.1:n.334A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inflammatory bowel disease
Identifiers:: MONDO: MONDO:0005265; MedGen: C0021390; OMIM: PS266600

Recent activity

Clear Turn Off Turn On

amidase [Gloeothece verrucosa]
amidase [Gloeothece verrucosa]
gi|503089863|ref|WP_013324706.1|

Protein
Mus musculus diacylglycerol kinase, beta (Dgkb), transcript variant 1, mRNA
Mus musculus diacylglycerol kinase, beta (Dgkb), transcript variant 1, mRNA
gi|1371986072|ref|NM_001361686.1|

Nucleotide
synapsin-3 isoform X7 [Mus musculus]
synapsin-3 isoform X7 [Mus musculus]
gi|1720361451|ref|XP_030100963.1|

Protein
PREDICTED: Homo sapiens TBC1 domain family member 32 (TBC1D32), transcript varia...
PREDICTED: Homo sapiens TBC1 domain family member 32 (TBC1D32), transcript variant X12, mRNA
gi|2217360045|ref|XM_047418316.1|

Nucleotide
PREDICTED: Homo sapiens TBC1 domain family member 32 (TBC1D32), transcript varia...
PREDICTED: Homo sapiens TBC1 domain family member 32 (TBC1D32), transcript variant X18, mRNA
gi|2217360054|ref|XM_011535585.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001380202	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 31, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30290665, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001380202

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 31, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Targeted high-throughput sequencing technique for the molecular diagnosis of primary immunodeficiency disorders.

Chi ZH, Wei W, Bu DF, Li HH, Ding F, Zhu P.

Medicine (Baltimore). 2018 Oct;97(40):e12695. doi: 10.1097/MD.0000000000012695.

PubMed [citation]

PMID:: 30290665
PMCID:: PMC6200533

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, SCV001380202.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces glutamic acid with aspartic acid at codon 169 of the IL10 protein (p.Glu169Asp). The glutamic acid residue is moderately conserved and there is a small physicochemical difference between glutamic acid and aspartic acid. This variant is present in population databases (rs568879359, ExAC 0.01%). This missense change has been observed in individual(s) with a primary immunodeficiency disorder (PMID: 30290665). ClinVar contains an entry for this variant (Variation ID: 939398). 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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: Sep 29, 2024

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Relating variation to medicine