NM_003954.5(MAP3K14):c.2437C>A (p.Pro813Thr) AND NIK deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 13, 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:: RCV003088901.1

Allele description [Variation Report for NM_003954.5(MAP3K14):c.2437C>A (p.Pro813Thr)]

NM_003954.5(MAP3K14):c.2437C>A (p.Pro813Thr)

Genes:

LOC126862575:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:43344006-43345205 [Gene]
MAP3K14-AS1:MAP3K14 antisense RNA 1 [Gene - HGNC]
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.2437C>A (p.Pro813Thr)

HGVS:

NC_000017.11:g.45266678G>T
NG_033823.1:g.55371C>A
NG_087072.1:g.140G>T
NM_003954.5:c.2437C>AMANE SELECT
NP_003945.2:p.Pro813Thr
LRG_1222t1:c.2437C>A
LRG_1222:g.55371C>A
LRG_1222p1:p.Pro813Thr
NC_000017.10:g.43344045G>T

Protein change:

P813T

Molecular consequence:

NM_003954.5:c.2437C>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
SCV003486030	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 13, 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

SCV003486030

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 13, 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003486030.1

#	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 proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 813 of the MAP3K14 protein (p.Pro813Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with MAP3K14-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Dec 24, 2023

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