14-23321471-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC

Variant names:

• chr14-23321471-T-TGGCGGCGGCGGCGGCGGC
• rs193922941
• NM_004643.4:c.6_23dupGGCGGCGGCGGCGGCGGC

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PP5_Moderate BP3

The NM_004643.4(PABPN1):​c.6_23dupGGCGGCGGCGGCGGCGGC​(p.Ala3_Ala8dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. A8A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PABPN1 NM_004643.4 disruptive_inframe_insertion
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 2.81
• Publications: 1 publications found

Genes affected

PABPN1 (HGNC:8565): (poly(A) binding protein nuclear 1) This gene encodes an abundant nuclear protein that binds with high affinity to nascent poly(A) tails. The protein is required for progressive and efficient polymerization of poly(A) tails at the 3' ends of eukaryotic transcripts and controls the size of the poly(A) tail to about 250 nt. At steady-state, this protein is localized in the nucleus whereas a different poly(A) binding protein is localized in the cytoplasm. This gene contains a GCG trinucleotide repeat at the 5' end of the coding region, and expansion of this repeat from the normal 6 copies to 8-13 copies leads to autosomal dominant oculopharyngeal muscular dystrophy (OPMD) disease. Related pseudogenes have been identified on chromosomes 19 and X. Read-through transcription also exists between this gene and the neighboring upstream BCL2-like 2 (BCL2L2) gene. [provided by RefSeq, Dec 2010]

BCL2L2-PABPN1 (HGNC:42959): (BCL2L2-PABPN1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring BCL2L2 (BCL2-like 2) and PABPN1 (poly(A) binding protein, nuclear 1) genes on chromosome 14. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP5: Variant 14-23321471-T-TGGCGGCGGCGGCGGCGGC is Pathogenic according to our data. Variant chr14-23321471-T-TGGCGGCGGCGGCGGCGGC is described in ClinVar as Pathogenic. ClinVar VariationId is 3907692.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP3: Nonframeshift variant in repetitive region in NM_004643.4

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004643.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABPN1	NM_004643.4	MANE Select	c.6_23dupGGCGGCGGCGGCGGCGGC	p.Ala3_Ala8dup	disruptive_inframe_insertion	Exon 1 of 7	NP_004634.1	Q86U42-1
	PABPN1	NM_001360551.3		c.6_23dupGGCGGCGGCGGCGGCGGC	p.Ala3_Ala8dup	disruptive_inframe_insertion	Exon 1 of 6	NP_001347480.1	Q86U42-2
	BCL2L2-PABPN1	NM_001387340.1		c.550-706_550-689dupGGCGGCGGCGGCGGCGGC		intron	N/A	NP_001374269.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PABPN1	ENST00000216727.9	TSL:1 MANE Select	c.6_23dupGGCGGCGGCGGCGGCGGC	p.Ala3_Ala8dup	disruptive_inframe_insertion	Exon 1 of 7	ENSP00000216727.4	Q86U42-1
	PABPN1	ENST00000397276.6	TSL:1	c.6_23dupGGCGGCGGCGGCGGCGGC	p.Ala3_Ala8dup	disruptive_inframe_insertion	Exon 1 of 6	ENSP00000380446.2	Q86U42-2
	BCL2L2-PABPN1	ENST00000553781.5	TSL:2	c.433-706_433-689dupGGCGGCGGCGGCGGCGGC		intron	N/A	ENSP00000451320.1	Q92843-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Oculopharyngeal muscular dystrophy 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs193922941; hg19: chr14-23790680;