rs137853321

Variant names:

• chrX-154564460-A-G
• rs137853321
• NM_001099857.5:c.1259A>G

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM4 PP5

The NM_001099857.5(IKBKG):​c.1259A>G​(p.Ter420Trpext*?) variant causes a stop lost change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 0)
• Consequence: IKBKG NM_001099857.5 stop_lost
• Clinical Significance: Pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 4.35
• Publications: 9 publications found

Genes affected

IKBKG (HGNC:5961): (inhibitor of nuclear factor kappa B kinase regulatory subunit gamma) This gene encodes the regulatory subunit of the inhibitor of kappaB kinase (IKK) complex, which activates NF-kappaB resulting in activation of genes involved in inflammation, immunity, cell survival, and other pathways. Mutations in this gene result in incontinentia pigmenti, hypohidrotic ectodermal dysplasia, and several other types of immunodeficiencies. A pseudogene highly similar to this locus is located in an adjacent region of the X chromosome. [provided by RefSeq, Mar 2016]

IKBKG Gene-Disease associations (from GenCC):

• ectodermal dysplasia and immunodeficiency 1

  Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
• IKBKG-related immunodeficiency with or without ectodermal dysplasia

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• incontinentia pigmenti

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Genomics England PanelApp, G2P, Orphanet
• ectodermal dysplasia and immune deficiency

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• anhidrotic ectodermal dysplasia-immunodeficiency-osteopetrosis-lymphedema syndrome

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• immunodeficiency 33

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM4: Stoplost variant in NM_001099857.5 Downstream stopcodon found after 466 codons.
• PP5: Variant X-154564460-A-G is Pathogenic according to our data. Variant chrX-154564460-A-G is described in ClinVar as Pathogenic. ClinVar VariationId is 11450.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099857.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IKBKG	NM_001099857.5	MANE Select	c.1259A>G	p.Ter420Trpext*?	stop_lost	Exon 10 of 10	NP_001093327.1
	IKBKG	NM_001099856.6		c.1463A>G	p.Ter488Trpext*?	stop_lost	Exon 10 of 10	NP_001093326.2
	IKBKG	NM_001321396.3		c.1259A>G	p.Ter420Trpext*?	stop_lost	Exon 10 of 10	NP_001308325.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IKBKG	ENST00000594239.6	TSL:1 MANE Select	c.1259A>G	p.Ter420Trpext*?	stop_lost	Exon 10 of 10	ENSP00000471166.1
	IKBKG	ENST00000618670.4	TSL:1	c.1463A>G	p.Ter488Trpext*?	stop_lost	Exon 10 of 10	ENSP00000483825.1
	IKBKG	ENST00000611071.4	TSL:1	c.1259A>G	p.Ter420Trpext*?	stop_lost	Exon 10 of 10	ENSP00000479662.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	ECTODERMAL DYSPLASIA AND IMMUNODEFICIENCY 1, MALE-RESTRICTED (1)
1	-	-	Incontinentia pigmenti syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.84
FATHMM_MKL	Benign	0.37	N
PhyloP100		4.3
Vest4		0.45
GERP RS		2.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs137853321; hg19: chrX-153792675;