4-38828729-A-T

Variant names:

• chr4-38828729-A-T
• rs5743810
• NM_006068.5:c.745T>A
• TLR6 p.Ser249Thr

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

0 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 0 classification points (ACMG Germline Pathogenicity v2019). PM2BP4_Moderate

The NM_006068.5(TLR6):c.745T>A (p.Ser249Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.S249A: protective (ClinVar VariationId 1710535, 0 stars)

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TLR6 NM_006068.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.928
• Publications: 33 publications found

Genes affected

TLR6 (HGNC:16711): (toll like receptor 6) The protein encoded by this gene is a member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. The various TLRs exhibit different patterns of expression. This receptor functionally interacts with toll-like receptor 2 to mediate cellular response to bacterial lipoproteins. A Ser249Pro polymorphism in the extracellular domain of the encoded protein may be associated with an increased of asthma is some populations.[provided by RefSeq, Jan 2011]

TLR1 (HGNC:11847): (toll like receptor 1) The protein encoded by this gene is a member of the Toll-like receptor (TLR) family which plays a fundamental role in pathogen recognition and activation of innate immunity. TLRs are highly conserved from Drosophila to humans and share structural and functional similarities. They recognize pathogen-associated molecular patterns (PAMPs) that are expressed on infectious agents, and mediate the production of cytokines necessary for the development of effective immunity. The various TLRs exhibit different patterns of expression. This gene is ubiquitously expressed, and at higher levels than other TLR genes. Different length transcripts presumably resulting from use of alternative polyadenylation site, and/or from alternative splicing, have been noted for this gene. [provided by RefSeq, Jul 2008]

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 0 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Moderate).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_006068.5. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	TLR6 NM_006068.5	MANE Select	c.745T>A p.Ser249Thr	missense	Exon 2 of 2	Prot: NP_006059.2
	TLR6 NM_001394553.1		c.745T>A p.Ser249Thr	missense	Exon 2 of 2	Prot: NP_001381482.1 UniProt:

TLR6 NM_006068.5

MANE Select

HGVSc / HGVSpc.745T>Ap.Ser249Thr

Exon rankExon 2 of 2

missense

Prot: NP_006059.2

TLR6 NM_001394553.1

HGVSc / HGVSpc.745T>Ap.Ser249Thr

Exon rankExon 2 of 2

missense

Prot: NP_001381482.1UniProt: Q9Y2C9-1

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	TLR6 ENST00000508254.6	TSL:1MANE Select	c.745T>A p.Ser249Thr	missense	Exon 2 of 2	Prot: ENSP00000424718.2 UniProt:
	TLR6 ENST00000381950.2	TSL:6	c.745T>A p.Ser249Thr	missense	Exon 3 of 3	Prot: ENSP00000371376.1 UniProt:
	TLR6 ENST00000966018.1		c.745T>A p.Ser249Thr	missense	Exon 2 of 2	Prot: ENSP00000636077.1 UniProt:

TLR6 ENST00000508254.6

TSL:1MANE Select

HGVSc / HGVSpc.745T>Ap.Ser249Thr

Exon rankExon 2 of 2

missense

Prot: ENSP00000424718.2UniProt: Q9Y2C9-1

TLR6 ENST00000381950.2

TSL:6

HGVSc / HGVSpc.745T>Ap.Ser249Thr

Exon rankExon 3 of 3

missense

Prot: ENSP00000371376.1UniProt: Q9Y2C9-1

TLR6 ENST00000966018.1

HGVSc / HGVSpc.745T>Ap.Ser249Thr

Exon rankExon 2 of 2

missense

Prot: ENSP00000636077.1UniProt: Q9Y2C9-1

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome Warning	AF: 0.00	AC:0	Hom:0	AN:1461684	Cov:49
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Uncertain	16
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	5.2
DANN	Benign	0.62
DEOGEN2	Benign	0.071	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.16	N
FuncVEP CTI	Benign	0.021
GPN-Star LLR	N/A	-0.35
GPN-Star score	N/A	0.35
LIST_S2	Benign	0.59	T
M_CAP	Benign	0.0069	T
MetaRNN	Benign	0.066	T
MetaSVM	Benign	-1.0	T
Mutation Taster	N/A	96/4	polymorphism
MutationAssessor	Benign	1.2	L
PhyloP100	Benign	0.93
popEVE	Benign	-2.9
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.67	N
REVEL	Benign	0.040
Sift	Benign	0.55	T
Sift4G	Benign	0.59	T
Varity_R	N/A	0.025
VESM-3B	Benign	-4.2

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs5743810;

hg19: chr4-38830350;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar