3-100744917-G-T

Variant names:

• chr3-100744917-G-T
• rs587777789
• NM_006070.6:c.806G>T

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PP3 PP5

The NM_006070.6(TFG):​c.806G>T​(p.Gly269Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TFG NM_006070.6 missense
• Clinical Significance: Pathogenic/Likely pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 5.43
• Publications: 19 publications found

Genes affected

TFG (HGNC:11758): (trafficking from ER to golgi regulator) There are several documented fusion oncoproteins encoded partially by this gene. This gene also participates in several oncogenic rearrangements resulting in anaplastic lymphoma and mixoid chondrosarcoma, and may play a role in the NF-kappaB pathway. Multiple transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]

TFG Gene-Disease associations (from GenCC):

• hereditary motor and sensory neuropathy, Okinawa type

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• hereditary spastic paraplegia 57

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• autosomal dominant Charcot-Marie-Tooth disease type 2 due to TFG mutation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.823
• PP5: Variant 3-100744917-G-T is Pathogenic according to our data. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-100744917-G-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156445.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TFG	NM_006070.6	c.806G>T	p.Gly269Val	missense_variant	Exon 7 of 8	ENST00000240851.9	NP_006061.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TFG	ENST00000240851.9	c.806G>T	p.Gly269Val	missense_variant	Exon 7 of 8	1	NM_006070.6	ENSP00000240851.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

Submissions by phenotype

Hereditary motor and sensory neuropathy, Okinawa type Pathogenic:1

Sep 02, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Hereditary spastic paraplegia 57 Pathogenic:1

Jun 01, 2022

Solve-RD Consortium

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: provider interpretation

Variant confirmed as disease-causing by referring clinical team -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.53
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.54	.;.;D;D;.;.
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	.;.;.;D;D;D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.82	D;D;D;D;D;D
MetaSVM	Benign	-0.39	T
MutationAssessor	Uncertain	2.0	M;.;M;M;.;M
PhyloP100		5.4
PrimateAI	Uncertain	0.58	T
PROVEAN	Uncertain	-3.1	.;D;D;D;D;.
REVEL	Pathogenic	0.68
Sift	Uncertain	0.0050	.;D;D;D;D;.
Sift4G	Uncertain	0.030	D;D;D;D;D;D
Polyphen		0.91	.;.;P;P;.;.
Vest4		0.71
MutPred		0.48		Loss of glycosylation at P265 (P = 0.0107);.;Loss of glycosylation at P265 (P = 0.0107);Loss of glycosylation at P265 (P = 0.0107);.;Loss of glycosylation at P265 (P = 0.0107);
MVP		0.28
MPC		1.3
ClinPred		0.97	D
GERP RS		5.9
Varity_R		0.40
gMVP		0.24
Mutation Taster		=9/91	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.46		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.46		Position offset: -6

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

Other links and lift over

dbSNP: rs587777789; hg19: chr3-100463761;