11-45910171-TGGGACGCTGCCGGAGTCAGTTTTATTAGGGAAGAGGGGCTCCCTGCCCCACCCCTCCCCACACCCTCCTTCCGGGAGGTCTGTCAGCCCCAACTGTAGAAGTAGATTTTCTGCCAGGTGGGCAAGTAATCCATGAGCGGCCCTGCAGTGGGAGAGGGACACATCAGGGCAGGCCAGACCCCAATCTGCACTGTGGCGCCACATACAGCACCTCACCCCTGCGGCCCAGGAGCCAGCCCAGCTGGCTGTCTTGCCCTGCCCCCAGGAGGCAGCACTGCAGGGGACTCTGGCACCATTTACAAAGACCCTCAGGCCCAGAGAAGCTCAGCCAGGGTAGACACTGAGGGGCCTGAGTCAGGTCCAGTCACCCAACCCAAGCCCAGTGGGCCTCTGCTGAGGGAGGATCTCAGCAGCCCGGTGGACCCCTTCTCTGCCATTGAATCCCCCCAAGATGAGATGGTCCCGTATCGCTCCAGGATACTGTGACCAGAAAAAAGCTGGCAGCTGATGTGGTCCCCCCACCAGTGGACACCCTCCTTCCAGCCATCCCTGGCTCCTCAGGCCACCCTGGCCTATGCCCAGGGGCAGTCCCACCCAATCCTGACTTCCC-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_004813.4(PEX16):c.952+118_*82del variant causes a splice acceptor, coding sequence, 3 prime UTR, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PEX16 NM_004813.4 splice_acceptor, coding_sequence, 3_prime_UTR, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.64

Genes affected

PEX16 (HGNC:8857): (peroxisomal biogenesis factor 16) The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease,
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-45910171-TGGGACGCTGCCGGAGTCAGTTTTATTAGGGAAGAGGGGCTCCCTGCCCCACCCCTCCCCACACCCTCCTTCCGGGAGGTCTGTCAGCCCCAACTGTAGAAGTAGATTTTCTGCCAGGTGGGCAAGTAATCCATGAGCGGCCCTGCAGTGGGAGAGGGACACATCAGGGCAGGCCAGACCCCAATCTGCACTGTGGCGCCACATACAGCACCTCACCCCTGCGGCCCAGGAGCCAGCCCAGCTGGCTGTCTTGCCCTGCCCCCAGGAGGCAGCACTGCAGGGGACTCTGGCACCATTTACAAAGACCCTCAGGCCCAGAGAAGCTCAGCCAGGGTAGACACTGAGGGGCCTGAGTCAGGTCCAGTCACCCAACCCAAGCCCAGTGGGCCTCTGCTGAGGGAGGATCTCAGCAGCCCGGTGGACCCCTTCTCTGCCATTGAATCCCCCCAAGATGAGATGGTCCCGTATCGCTCCAGGATACTGTGACCAGAAAAAAGCTGGCAGCTGATGTGGTCCCCCCACCAGTGGACACCCTCCTTCCAGCCATCCCTGGCTCCTCAGGCCACCCTGGCCTATGCCCAGGGGCAGTCCCACCCAATCCTGACTTCCC-T is Pathogenic according to our data. Variant chr11-45910171-TGGGACGCTGCCGGAGTCAGTTTTATTAGGGAAGAGGGGCTCCCTGCCCCACCCCTCCCCACACCCTCCTTCCGGGAGGTCTGTCAGCCCCAACTGTAGAAGTAGATTTTCTGCCAGGTGGGCAAGTAATCCATGAGCGGCCCTGCAGTGGGAGAGGGACACATCAGGGCAGGCCAGACCCCAATCTGCACTGTGGCGCCACATACAGCACCTCACCCCTGCGGCCCAGGAGCCAGCCCAGCTGGCTGTCTTGCCCTGCCCCCAGGAGGCAGCACTGCAGGGGACTCTGGCACCATTTACAAAGACCCTCAGGCCCAGAGAAGCTCAGCCAGGGTAGACACTGAGGGGCCTGAGTCAGGTCCAGTCACCCAACCCAAGCCCAGTGGGCCTCTGCTGAGGGAGGATCTCAGCAGCCCGGTGGACCCCTTCTCTGCCATTGAATCCCCCCAAGATGAGATGGTCCCGTATCGCTCCAGGATACTGTGACCAGAAAAAAGCTGGCAGCTGATGTGGTCCCCCCACCAGTGGACACCCTCCTTCCAGCCATCCCTGGCTCCTCAGGCCACCCTGGCCTATGCCCAGGGGCAGTCCCACCCAATCCTGACTTCCC-T is described in ClinVar as [Pathogenic]. Clinvar id is 30353.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PEX16	NM_004813.4	c.952+118_*82del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	11/11	ENST00000378750.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PEX16	ENST00000378750.10	c.952+118_*82del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	11/11	1	NM_004813.4	P1
PEX16	ENST00000241041.7	c.952+118_958del		splice_acceptor_variant, coding_sequence_variant, intron_variant	11/11	1
PEX16	ENST00000532681.5			splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	11/11	3
PEX16	ENST00000523721.2	n.182+118_323del		splice_acceptor_variant, non_coding_transcript_exon_variant, intron_variant	3/3	5

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Peroxisome biogenesis disorder 8B Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 01, 2010

- -

Computational scores

Source: dbNSFP v4.3

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: chr11-45931722;