11-66070587-CGCAGCAGCA-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_018026.4(PACS1):​c.113_121delAGCAGCAGC​(p.Gln38_Gln40del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000119 in 1,342,466 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )

Consequence

PACS1
NM_018026.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.79
Variant links:
Genes affected
PACS1 (HGNC:30032): (phosphofurin acidic cluster sorting protein 1) This gene encodes a protein with a putative role in the localization of trans-Golgi network (TGN) membrane proteins. Mouse and rat homologs have been identified and studies of the homologous rat protein indicate a role in directing TGN localization of furin by binding to the protease's phosphorylated cytosolic domain. In addition, the human protein plays a role in HIV-1 Nef-mediated downregulation of cell surface MHC-I molecules to the TGN, thereby enabling HIV-1 to escape immune surveillance. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAdExome4 at 16 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PACS1NM_018026.4 linkc.113_121delAGCAGCAGC p.Gln38_Gln40del disruptive_inframe_deletion Exon 1 of 24 ENST00000320580.9 NP_060496.2 Q6VY07-1A0A024R5H6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PACS1ENST00000320580.9 linkc.113_121delAGCAGCAGC p.Gln38_Gln40del disruptive_inframe_deletion Exon 1 of 24 1 NM_018026.4 ENSP00000316454.4 Q6VY07-1
PACS1ENST00000527224.1 linkn.237_245delAGCAGCAGC non_coding_transcript_exon_variant Exon 1 of 7 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.0000119
AC:
16
AN:
1342466
Hom.:
0
AF XY:
0.0000136
AC XY:
9
AN XY:
663130
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000632
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:
0.0000123
Gnomad4 OTH exome
AF:
0.0000179
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Schuurs-Hoeijmakers syndrome Uncertain:1
Feb 09, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with PACS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.113_121del, results in the deletion of 3 amino acid(s) of the PACS1 protein (p.Gln38_Gln40del), but otherwise preserves the integrity of the reading frame. -

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-65838058; API