NM_001292063.2:c.1793G>T

Variant names:

• chr11-17570228-G-T
• NM_001292063.2:c.1793G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001292063.2(OTOG):​c.1793G>T​(p.Arg598Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,398,396 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/20 in silico tools predict 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: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: OTOG NM_001292063.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56

Genes affected

OTOG (HGNC:8516): (otogelin) The protein encoded by this gene is a component of the acellular membranes of the inner ear. Disruption of the orthologous mouse gene shows that it plays a role in auditory and vestibular functions. It is involved in fibrillar network organization, the anchoring of otoconial membranes and cupulae to the neuroepithelia, and likely in sound stimulation resistance. Mutations in this gene cause autosomal recessive nonsyndromic deafness, type 18B. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OTOG	NM_001292063.2	c.1793G>T	p.Arg598Leu	missense_variant	Exon 17 of 56	ENST00000399397.6	NP_001278992.1
OTOG	NM_001277269.2	c.1829G>T	p.Arg610Leu	missense_variant	Exon 16 of 55		NP_001264198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTOG	ENST00000399397.6	c.1793G>T	p.Arg598Leu	missense_variant	Exon 17 of 56	5	NM_001292063.2	ENSP00000382329.2
OTOG	ENST00000399391.7	c.1829G>T	p.Arg610Leu	missense_variant	Exon 16 of 55	5		ENSP00000382323.2
OTOG	ENST00000498332.5	n.1699G>T		non_coding_transcript_exon_variant	Exon 16 of 16	5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1398396 Hom.: 0 Cov.: 30 AF XY: 0.00000290 AC XY: 2 AN XY: 689728

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.27e-7

Gnomad4 OTH exome AF: 0.0000172

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.0044	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.23	T;.
Eigen	Benign	-0.056
Eigen_PC	Benign	-0.022
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Benign	0.045	D
MetaRNN	Uncertain	0.67	D;D
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	1.6	L;.
PrimateAI	Benign	0.44	T
PROVEAN	Pathogenic	-4.8	D;.
REVEL	Uncertain	0.40
Sift	Uncertain	0.013	D;.
Sift4G	Uncertain	0.0050	D;D
Vest4		0.57
MutPred		0.76		Loss of methylation at R610 (P = 0.0471);.;
MVP		0.56
ClinPred		0.97	D
GERP RS		2.8
Varity_R		0.33
gMVP		0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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: chr11-17591775;