rs104893855

Positions:

• chr4-41747479-C-A
• chr4-41747479-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1 PM2 PP3_Strong PP5

The ENST00000226382.4(PHOX2B):​c.299G>T​(p.Arg100Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R100H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: PHOX2B ENST00000226382.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1 O:1
• Conservation: PhyloP100: 7.86

Genes affected

PHOX2B (HGNC:9143): (paired like homeobox 2B) The DNA-associated protein encoded by this gene is a member of the paired family of homeobox proteins localized to the nucleus. The protein functions as a transcription factor involved in the development of several major noradrenergic neuron populations and the determination of neurotransmitter phenotype. The gene product is linked to enhancement of second messenger-mediated activation of the dopamine beta-hydroylase, c-fos promoters and several enhancers, including cyclic amp-response element and serum-response element. Expansion of a 20 amino acid polyalanine tract in this protein by 5-13 aa has been associated with congenital central hypoventilation syndrome. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM1: In a DNA_binding_region Homeobox (size 59) in uniprot entity PHX2B_HUMAN there are 14 pathogenic changes around while only 1 benign (93%) in ENST00000226382.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.99
• PP5: Variant 4-41747479-C-A is Pathogenic according to our data. Variant chr4-41747479-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 6011.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHOX2B	NM_003924.4	c.299G>T	p.Arg100Leu	missense_variant	2/3	ENST00000226382.4	NP_003915.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHOX2B	ENST00000226382.4	c.299G>T	p.Arg100Leu	missense_variant	2/3	1	NM_003924.4	ENSP00000226382	P1
PHOX2B	ENST00000510424.2	n.120G>T		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 28, 2016

The p.R100L variant (also known as c.299G>T), located in coding exon 2 of the PHOX2B gene, results from a G to T substitution at nucleotide position 299. The arginine at codon 100 is replaced by leucine, an amino acid with dissimilar properties. This variant was identified in three individuals of one family with tumors of neural crest origin; the proband had a multifocal abdominal ganglioneuroma removed at age 10, a sibling had an abdominal neuroblastoma removed at age 6 and two recurrences, and their father had a ganglioneuroma of the adrenal medulla removed at age 44. Two paternal first cousins with Hirschsprung disease also had this alteration, as well as two unaffected paternal relatives (Trochet D et al. Am. J. Hum. Genet., 2004 Apr;74:761-4; Bourdeaut F et al. Cancer Lett., 2005 Oct;228:51-8). In vitro analysis of the protein with this alteration demonstrated complete loss of DNA binding (Trochet D et al. Hum. Mol. Genet., 2005 Dec;14:3697-708). This variant was previously reported in the SNPDatabase as rs104893855. This variant was not reported in population-based cohorts in the following databases: NHLBI Exome Sequencing Project (ESP) and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Haddad syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 31, 2017

This sequence change replaces arginine with leucine at codon 100 of the PHOX2B protein (p.Arg100Leu). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and leucine. In summary, this variant impacts PHOX2B function and has been observed in affected individual. However, the available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies demonstrate that this missense change impedes the DNA binding and transactivation activity of PHOX2B and suppresses cellular differentiation, but nuclear localization and cell proliferation are not affected (PMID: 16249188, 19058226, 23873030, 17637745). This variant has been reported to segregate with Hirschsprung disease and neuroblastic tumors in a single family (PMID: 15949893, 15024693). It has also been observed in an individual affected with sporadic congenital central hypoventilation syndrome (PMID: 17637745). ClinVar contains an entry for this variant (Variation ID: 6011). This variant is not present in population databases (ExAC no frequency). -

Neuroblastoma, susceptibility to, 2 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Apr 01, 2004

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.97	D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.98
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.96	D
M_CAP	Pathogenic	0.60	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.2	H
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.94	D
PROVEAN	Pathogenic	-6.5	D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0030	D
Polyphen		1.0	D
Vest4		0.93
MutPred		0.93		Loss of disorder (P = 0.0377);
MVP		0.98
MPC		2.6
ClinPred		1.0	D
GERP RS		5.4
Varity_R		0.94
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs104893855; hg19: chr4-41749496;