rs11832772

Variant names:

• chr12-42465786-C-A
• rs11832772
• ENST00000547824.1:n.2449C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-42465786-C-A
• chr12-42465786-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000547824.1(ENSG00000257225):​n.2449C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000257225 ENST00000547824.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 21 publications found

Genes affected

ENSG00000257225 (HGNC:58444):

PRICKLE1 (HGNC:17019): (prickle planar cell polarity protein 1) This gene encodes a nuclear receptor that may be a negative regulator of the Wnt/beta-catenin signaling pathway. The encoded protein localizes to the nuclear membrane and has been implicated in the nuclear trafficking of the transcription repressors REST/NRSF and REST4. Mutations in this gene have been linked to progressive myoclonus epilepsy. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Sep 2009]

PRICKLE1 Gene-Disease associations (from GenCC):

• epilepsy, progressive myoclonic, 1B

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• Unverricht-Lundborg syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• progressive myoclonus epilepsy

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen
• epilepsy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547824.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRICKLE1	NM_153026.3	MANE Select	c.775+408G>T		intron	N/A	NP_694571.2
	PRICKLE1	NM_001144881.2		c.775+408G>T		intron	N/A	NP_001138353.1
	PRICKLE1	NM_001144882.2		c.775+408G>T		intron	N/A	NP_001138354.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257225	ENST00000547824.1	TSL:1	n.2449C>A		non_coding_transcript_exon	Exon 2 of 2
	PRICKLE1	ENST00000345127.9	TSL:1 MANE Select	c.775+408G>T		intron	N/A	ENSP00000345064.3
	PRICKLE1	ENST00000445766.7	TSL:5	c.775+408G>T		intron	N/A	ENSP00000398947.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 166766 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 89644

African (AFR) AF: 0.00 AC: 0 AN: 4858

American (AMR) AF: 0.00 AC: 0 AN: 6204

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4434

East Asian (EAS) AF: 0.00 AC: 0 AN: 7068

South Asian (SAS) AF: 0.00 AC: 0 AN: 27816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7732

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 640

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 99562

Other (OTH) AF: 0.00 AC: 0 AN: 8452

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 13088

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11832772; hg19: chr12-42859588;