chr12-110614164-C-T

Variant names:

• chr12-110614164-C-T
• rs773061089
• NM_001082538.3:c.-19C>T

Variant summary

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

The NM_001082538.3(TCTN1):​c.-19C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000501 in 1,395,918 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000050 (0 hom.)
• Consequence: TCTN1 NM_001082538.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 0 publications found

Genes affected

TCTN1 (HGNC:26113): (tectonic family member 1) This gene encodes a member of a family of secreted and transmembrane proteins. The orthologous gene in mouse functions downstream of smoothened and rab23 to modulate hedgehog signal transduction. This protein is a component of the tectonic-like complex, which forms a barrier between the ciliary axoneme and the basal body. A mutation in this gene was found in a family with Joubert syndrome-13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

TCTN1 Gene-Disease associations (from GenCC):

• Joubert syndrome 13

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• Joubert syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Meckel syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

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=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCTN1	NM_001082538.3	c.-19C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 15	ENST00000397659.9	NP_001076007.1
TCTN1	NM_001082538.3	c.-19C>T		5_prime_UTR_variant	Exon 1 of 15	ENST00000397659.9	NP_001076007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCTN1	ENST00000397659.9	c.-19C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 15	1	NM_001082538.3	ENSP00000380779.4
TCTN1	ENST00000551590.5	c.-19C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 15	1		ENSP00000448735.1
TCTN1	ENST00000397655.7	c.-19C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 15	1		ENSP00000380775.3
TCTN1	ENST00000397656.8	n.-19C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 16	2		ENSP00000380776.4
TCTN1	ENST00000495659.6	n.-19C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 15	2		ENSP00000436673.2
TCTN1	ENST00000397656.8	n.-19C>T		non_coding_transcript_exon_variant	Exon 1 of 16	2		ENSP00000380776.4
TCTN1	ENST00000495659.6	n.-19C>T		non_coding_transcript_exon_variant	Exon 1 of 15	2		ENSP00000436673.2
TCTN1	ENST00000397659.9	c.-19C>T		5_prime_UTR_variant	Exon 1 of 15	1	NM_001082538.3	ENSP00000380779.4
TCTN1	ENST00000551590.5	c.-19C>T		5_prime_UTR_variant	Exon 1 of 15	1		ENSP00000448735.1
TCTN1	ENST00000397655.7	c.-19C>T		5_prime_UTR_variant	Exon 1 of 15	1		ENSP00000380775.3
TCTN1	ENST00000397656.8	n.-19C>T		5_prime_UTR_variant	Exon 1 of 16	2		ENSP00000380776.4
TCTN1	ENST00000495659.6	n.-19C>T		5_prime_UTR_variant	Exon 1 of 15	2		ENSP00000436673.2
TCTN1	ENST00000480648.5	n.-19C>T		upstream_gene_variant		5		ENSP00000437196.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000501 AC: 7 AN: 1395918 Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1 AN XY: 688652

African (AFR) AF: 0.00 AC: 0 AN: 31862

American (AMR) AF: 0.00 AC: 0 AN: 35772

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25154

East Asian (EAS) AF: 0.00 AC: 0 AN: 36254

South Asian (SAS) AF: 0.00 AC: 0 AN: 79264

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46194

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4110

European-Non Finnish (NFE) AF: 0.00000556 AC: 6 AN: 1079462

Other (OTH) AF: 0.0000173 AC: 1 AN: 57846

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.7
DANN	Benign	0.69
PhyloP100		-0.52
PromoterAI		0.040	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs773061089; hg19: chr12-111051969;