17-8173376-CCCAGTCAGAACTTCATAGCTATGTTTGTGGATATCTGCTAATCAGCATAACACAAATGTAAGTGATCGTCAGAAAGAATCAGACAGGAGCAATCAGGGTGTTGCAAGTCCTGATTACGCAGAGACGTTAATCACGTTTCATGCATCTCCAATCATCATGTTCTAATCTGCCCTCCGGAGGAGGAACAGGTAAGGATTATCCCACCTGACGATACAGACAAACAGCCGACATTCTGCACTCAGTGAAAAAGATTCCGTTACAAGCTAGGGTGAGTTCATAACG-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_183065.4(TMEM107):c.*545_*826del variant causes a 3 prime UTR 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: TMEM107 NM_183065.4 3_prime_UTR
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.943

Genes affected

TMEM107 (HGNC:28128): (transmembrane protein 107) This gene encodes a transmembrane protein and component of the primary cilia transition zone. The encoded protein regulates ciliogenesis and ciliary protein composition. Human fibroblasts expressing a mutant allele of this gene exhibit reduced numbers of cilia, altered cilia length, and impaired sonic hedgehog signaling. In human patients, different mutations in this gene cause different ciliopathies, including Meckel-Gruber syndrome and orofaciodigital syndrome. [provided by RefSeq, May 2017]

SNORD118 (HGNC:32952): (small nucleolar RNA, C/D box 118)

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-8173376-CCCAGTCAGAACTTCATAGCTATGTTTGTGGATATCTGCTAATCAGCATAACACAAATGTAAGTGATCGTCAGAAAGAATCAGACAGGAGCAATCAGGGTGTTGCAAGTCCTGATTACGCAGAGACGTTAATCACGTTTCATGCATCTCCAATCATCATGTTCTAATCTGCCCTCCGGAGGAGGAACAGGTAAGGATTATCCCACCTGACGATACAGACAAACAGCCGACATTCTGCACTCAGTGAAAAAGATTCCGTTACAAGCTAGGGTGAGTTCATAACG-C is Pathogenic according to our data. Variant chr17-8173376-CCCAGTCAGAACTTCATAGCTATGTTTGTGGATATCTGCTAATCAGCATAACACAAATGTAAGTGATCGTCAGAAAGAATCAGACAGGAGCAATCAGGGTGTTGCAAGTCCTGATTACGCAGAGACGTTAATCACGTTTCATGCATCTCCAATCATCATGTTCTAATCTGCCCTCCGGAGGAGGAACAGGTAAGGATTATCCCACCTGACGATACAGACAAACAGCCGACATTCTGCACTCAGTGAAAAAGATTCCGTTACAAGCTAGGGTGAGTTCATAACG-C is described in ClinVar as [Pathogenic]. Clinvar id is 929299.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM107	NM_183065.4	c.*545_*826del		3_prime_UTR_variant	5/5	ENST00000437139.7
SNORD118	NR_033294.2			transcript_ablation	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM107	ENST00000437139.7	c.*545_*826del		3_prime_UTR_variant	5/5	1	NM_183065.4	P1
TMEM107	ENST00000449985.6	c.*594_*875del		3_prime_UTR_variant	2/2	1
SNORD118	ENST00000363593.1			transcript_ablation	1/1

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

Leukoencephalopathy with calcifications and cysts Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine

Apr 06, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1983743862; hg19: chr17-8076694;