rs5885806

Variant names:

• chr7-92499847-CAAAA-C
• NM_000466.3:c.2584-13_2584-10delTTTT

Your query was ambiguous. Multiple possible variants found:

• chr7-92499847-CAAAA-C
• chr7-92499847-CAAAA-CA
• chr7-92499847-CAAAA-CAA
• chr7-92499847-CAAAA-CAAA
• chr7-92499847-CAAAA-CAAAAA
• chr7-92499847-CAAAA-CAAAAAA
• chr7-92499847-CAAAA-CAAAAAAA
• chr7-92499847-CAAAA-CAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000466.3(PEX1):​c.2584-13_2584-10delTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000764 in 1,178,704 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: 0)
  • Exomes 𝑓: 0.0000076 (0 hom.)
• Consequence: PEX1 NM_000466.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.05

Genes affected

PEX1 (HGNC:8850): (peroxisomal biogenesis factor 1) This gene encodes a member of the AAA ATPase family, a large group of ATPases associated with diverse cellular activities. This protein is cytoplasmic but is often anchored to a peroxisomal membrane where it forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis. Mutations in this gene have been associated with complementation group 1 peroxisomal disorders such as neonatal adrenoleukodystrophy, infantile Refsum disease, and Zellweger syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEX1	NM_000466.3	c.2584-13_2584-10delTTTT		intron_variant	Intron 15 of 23	ENST00000248633.9	NP_000457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEX1	ENST00000248633.9	c.2584-13_2584-10delTTTT		intron_variant	Intron 15 of 23	1	NM_000466.3	ENSP00000248633.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000764 AC: 9 AN: 1178704 Hom.: 0 AF XY: 0.0000118 AC XY: 7 AN XY: 592050

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: 0.0000276

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000794

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-92129161;