17-48801263-AAG-TAA

Variant names:

• chr17-48801263-AAG-TAA
• NM_001130918.3:c.601_603delCTTinsTTA
• TTLL6 p.202

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001130918.3(TTLL6):​c.601_603delCTTinsTTA​(p.202) variant causes a synonymous change involving the alteration of a 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 MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TTLL6 NM_001130918.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.92
• Publications: 0 publications found

Genes affected

TTLL6 (HGNC:26664): (tubulin tyrosine ligase like 6) Predicted to enable tubulin binding activity and tubulin-glutamic acid ligase activity. Predicted to be involved in microtubule cytoskeleton organization and protein polyglutamylation. Predicted to act upstream of or within microtubule bundle formation; microtubule severing; and positive regulation of cilium movement. Located in ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130918.3. 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
	TTLL6	NM_001130918.3	MANE Select	c.601_603delCTTinsTTA	p.202	synonymous	N/A	NP_001124390.1	Q8N841-1
	TTLL6	NM_001366314.2		c.142_144delCTTinsTTA	p.49	synonymous	N/A	NP_001353243.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTLL6	ENST00000393382.8	TSL:2 MANE Select	c.601_603delCTTinsTTA	p.202	synonymous	N/A	ENSP00000377043.3	Q8N841-1
	TTLL6	ENST00000376681.7	TSL:1	n.*644_*646delCTTinsTTA		non_coding_transcript_exon	Exon 5 of 14	ENSP00000365871.4	F8WDP8
	TTLL6	ENST00000490027.5	TSL:1	n.1425_1427delCTTinsTTA		non_coding_transcript_exon	Exon 4 of 16

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-46878625;