GeneBe

rs111688568

Variant names:

Variant summary

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

The NM_002637.4(PHKA1):​c.*1251_*1264delGTGTGTGTGTGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 19)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control

Consequence

PHKA1
NM_002637.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.05

Publications

0 publications found
Variant links:
Genes affected
PHKA1 (HGNC:8925): (phosphorylase kinase regulatory subunit alpha 1) Phosphorylase kinase is a polymer of 16 subunits, four each of alpha, beta, gamma and delta. The alpha subunit includes the skeletal muscle and hepatic isoforms, and the skeletal muscle isoform is encoded by this gene. The beta subunit is the same in both the muscle and hepatic isoforms, and encoded by one gene. The gamma subunit also includes the skeletal muscle and hepatic isoforms, which are encoded by two different genes. The delta subunit is a calmodulin and can be encoded by three different genes. The gamma subunits contain the active site of the enzyme, whereas the alpha and beta subunits have regulatory functions controlled by phosphorylation. The delta subunit mediates the dependence of the enzyme on calcium concentration. Mutations in this gene cause glycogen storage disease type 9D, also known as X-linked muscle glycogenosis. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. A pseudogene has been found on chromosome 1.[provided by RefSeq, Feb 2010]
PHKA1 Gene-Disease associations (from GenCC):
  • glycogen storage disease IXd
    Inheritance: XL, AR Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PHKA1NM_002637.4 linkc.*1251_*1264delGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 32 of 32 ENST00000373542.9 NP_002628.2 P46020-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PHKA1ENST00000373542.9 linkc.*1251_*1264delGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 32 of 32 1 NM_002637.4 ENSP00000362643.4 P46020-1
PHKA1ENST00000339490.7 linkc.*1251_*1264delGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 31 of 31 1 ENSP00000342469.3 P46020-2
PHKA1ENST00000541944.5 linkc.*1251_*1264delGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 30 of 30 1 ENSP00000441251.1 P46020-3
PHKA1ENST00000373545.7 linkc.*1251_*1264delGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 32 of 32 5 ENSP00000362646.3 A6NIT2

Frequencies

GnomAD3 genomes
Cov.:
19
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
36
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
22
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
33
Other (OTH)
AF:
0.00
AC:
0
AN:
3
GnomAD4 genome
Cov.:
19
Alfa
AF:
0.00
Hom.:
7
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs111688568; hg19: chrX-71799587; API