NM_001199138.2(NLRC4):c.1550G>C (p.Cys517Ser) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 2024
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:: RCV003774822.2

Allele description [Variation Report for NM_001199138.2(NLRC4):c.1550G>C (p.Cys517Ser)]

NM_001199138.2(NLRC4):c.1550G>C (p.Cys517Ser)

Gene:

NLRC4:NLR family CARD domain containing 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p22.3

Genomic location:

Preferred name:

NM_001199138.2(NLRC4):c.1550G>C (p.Cys517Ser)

HGVS:

NC_000002.12:g.32250314C>G
NG_041780.1:g.20430G>C
NM_001199138.2:c.1550G>CMANE SELECT
NM_001199139.1:c.1550G>C
NM_001302504.1:c.262+2105G>C
NM_021209.4:c.1550G>C
NP_001186067.1:p.Cys517Ser
NP_001186068.1:p.Cys517Ser
NP_067032.3:p.Cys517Ser
LRG_1317t1:c.1550G>C
LRG_1317:g.20430G>C
LRG_1317p1:p.Cys517Ser
NC_000002.11:g.32475383C>G

Protein change:

C517S

Links:

dbSNP: rs779390608

NCBI 1000 Genomes Browser:

rs779390608

Molecular consequence:

NM_001302504.1:c.262+2105G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001199138.2:c.1550G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001199139.1:c.1550G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_021209.4:c.1550G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Periodic fever-infantile enterocolitis-autoinflammatory syndrome
Synonyms:: Autoinflammation with infantile enterocolitis
Identifiers:: MONDO: MONDO:0014472; MedGen: C4015067; Orphanet: 436166; OMIM: 616050

Name:: Familial cold autoinflammatory syndrome 4 (FCAS4)
Identifiers:: MONDO: MONDO:0014498; MedGen: C4015276; Orphanet: 47045; OMIM: 616115

Recent activity

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arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2 isoform X...
arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2 isoform X14 [Homo sapiens]
gi|2462578188|ref|XP_054200363.1|

Protein
PREDICTED: Homo sapiens ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 (...
PREDICTED: Homo sapiens ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 (ASAP2), transcript variant X18, mRNA
gi|2462578195|ref|XM_054344392.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004571336	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 25, 2024)	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

SCV004571336

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 25, 2024)

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, SCV004571336.1

#	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 cysteine, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 517 of the NLRC4 protein (p.Cys517Ser). This variant is present in population databases (rs779390608, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with NLRC4-related conditions. ClinVar contains an entry for this variant (Variation ID: 1694363). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NLRC4 protein function with a negative predictive value of 80%. 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: Oct 20, 2024

ClinVar

Relating variation to medicine