11-72240115-GGCGCCCGCCGCGCCCGCC-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_005169.4(PHOX2A):​c.471_488delGGCGGGCGCGGCGGGCGC​(p.Ala158_Ala163del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000000725 in 1,379,908 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

PHOX2A
NM_005169.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.56
Variant links:
Genes affected
PHOX2A (HGNC:691): (paired like homeobox 2A) The protein encoded by this gene contains a paired-like homeodomain most similar to that of the Drosophila aristaless gene product. The encoded protein plays a central role in development of the autonomic nervous system. It regulates the expression of tyrosine hydroxylase and dopamine beta-hydroxylase, two catecholaminergic biosynthetic enzymes essential for the differentiation and maintenance of the noradrenergic neurotransmitter phenotype. The encoded protein has also been shown to regulate transcription of the alpha3 nicotinic acetylcholine receptor gene. Mutations in this gene have been associated with autosomal recessive congenital fibrosis of the extraocular muscles. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_005169.4.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PHOX2ANM_005169.4 linkc.471_488delGGCGGGCGCGGCGGGCGC p.Ala158_Ala163del disruptive_inframe_deletion Exon 3 of 3 ENST00000298231.5 NP_005160.2 O14813
PHOX2ANM_001425096.1 linkc.555_572delGGCGGGCGCGGCGGGCGC p.Ala186_Ala191del disruptive_inframe_deletion Exon 3 of 3 NP_001412025.1
PHOX2ANM_001425097.1 linkc.495_512delGGCGGGCGCGGCGGGCGC p.Ala166_Ala171del disruptive_inframe_deletion Exon 3 of 3 NP_001412026.1
PHOX2ANM_001425098.1 linkc.*350_*367delGGCGGGCGCGGCGGGCGC 3_prime_UTR_variant Exon 3 of 3 NP_001412027.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PHOX2AENST00000298231.5 linkc.471_488delGGCGGGCGCGGCGGGCGC p.Ala158_Ala163del disruptive_inframe_deletion Exon 3 of 3 1 NM_005169.4 ENSP00000298231.5 O14813
PHOX2AENST00000546310.1 linkc.85-214_85-197delGGCGGGCGCGGCGGGCGC intron_variant Intron 1 of 1 5 ENSP00000444845.1 H0YGU5
PHOX2AENST00000544057.1 linkn.339_356delGGCGGGCGCGGCGGGCGC non_coding_transcript_exon_variant Exon 3 of 3 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.25e-7
AC:
1
AN:
1379908
Hom.:
0
AF XY:
0.00000147
AC XY:
1
AN XY:
680768
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.29e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200556921; hg19: chr11-71951159; API