NM_003954.5(MAP3K14):c.1657G>A (p.Gly553Arg) AND NIK deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 12, 2022
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:: RCV000807656.6

Allele description [Variation Report for NM_003954.5(MAP3K14):c.1657G>A (p.Gly553Arg)]

NM_003954.5(MAP3K14):c.1657G>A (p.Gly553Arg)

Gene:

MAP3K14:mitogen-activated protein kinase kinase kinase 14 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_003954.5(MAP3K14):c.1657G>A (p.Gly553Arg)

HGVS:

NC_000017.11:g.45273503C>T
NG_033823.1:g.48546G>A
NM_003954.5:c.1657G>AMANE SELECT
NP_003945.2:p.Gly553Arg
LRG_1222t1:c.1657G>A
LRG_1222:g.48546G>A
LRG_1222p1:p.Gly553Arg
NC_000017.10:g.43350870C>T
NM_003954.4:c.1657G>A

Protein change:

G553R

Links:

dbSNP: rs1185307989

NCBI 1000 Genomes Browser:

rs1185307989

Molecular consequence:

NM_003954.5:c.1657G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: NIK deficiency
Synonyms:: Primary immunodeficiency with multifaceted aberrant lymphoid immunity
Identifiers:: MONDO: MONDO:0018642; MedGen: C5680065; Orphanet: 447731

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000947721	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 12, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000947721

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 12, 2022)

germline

clinical testing

PubMed (3)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000947721.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 652155). This variant has not been reported in the literature in individuals affected with MAP3K14-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 553 of the MAP3K14 protein (p.Gly553Arg). This variant also falls at the last nucleotide of exon 9, which is part of the consensus splice site for this exon.

#	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 14, 2024

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