chr1-235380119-C-G

Variant names:

• chr1-235380119-C-G
• rs750637765
• NM_003193.5:c.70C>G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_003193.5(TBCE):​c.70C>G​(p.Arg24Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R24H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: TBCE NM_003193.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965

Genes affected

TBCE (HGNC:11582): (tubulin folding cofactor E) Cofactor E is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ENSG00000285053 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.858

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBCE	NM_003193.5	c.70C>G	p.Arg24Gly	missense_variant	Exon 2 of 17	ENST00000642610.2	NP_003184.1
TBCE	NM_001287801.2	c.70C>G	p.Arg24Gly	missense_variant	Exon 2 of 18		NP_001274730.1
TBCE	NM_001079515.3	c.70C>G	p.Arg24Gly	missense_variant	Exon 2 of 17		NP_001072983.1
TBCE	NM_001287802.2	c.-241C>G		5_prime_UTR_variant	Exon 2 of 16		NP_001274731.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBCE	ENST00000642610.2	c.70C>G	p.Arg24Gly	missense_variant	Exon 2 of 17		NM_003193.5	ENSP00000494796.1
ENSG00000285053	ENST00000645655.1	c.70C>G	p.Arg24Gly	missense_variant	Exon 5 of 20			ENSP00000495202.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251438 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135892

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.0000992

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457460 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 725114

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000385

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

Alfa AF: 0.0000434 Hom.: 0

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Uncertain	0.070
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.77	D;D;D;D;D;.;.;D;D;D;.;.;.;.;.;.;.
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Uncertain	0.90	.;.;.;.;.;.;.;.;.;.;D;D;T;T;D;T;D
M_CAP	Uncertain	0.17	D
MetaRNN	Pathogenic	0.86	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.76	D
MutationAssessor	Pathogenic	3.5	H;H;H;H;H;.;.;H;H;H;.;.;.;.;H;.;.
PrimateAI	Benign	0.38	T
PROVEAN	Pathogenic	-4.9	.;.;.;.;.;.;.;.;.;D;.;.;.;.;D;D;.
REVEL	Pathogenic	0.72
Sift	Uncertain	0.010	.;.;.;.;.;.;.;.;.;D;.;.;.;.;D;D;.
Sift4G	Uncertain	0.0080	.;.;.;.;.;.;.;.;.;D;.;.;.;.;D;D;.
Polyphen		1.0	D;D;D;D;D;.;.;D;D;D;.;.;.;.;.;.;.
Vest4		0.80, 0.79
MutPred		0.78		Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);Loss of methylation at R24 (P = 0.0165);
MVP		0.93
MPC		0.89
ClinPred		0.94	D
GERP RS		4.6
Varity_R		0.29
gMVP		0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs750637765; hg19: chr1-235543434;