9-117704478-G-A

Variant names:

• chr9-117704478-G-A
• rs1005484206
• NM_138554.5:c.6G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_138554.5(TLR4):​c.6G>A​(p.Met2Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TLR4 NM_138554.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 0 publications found

Genes affected

TLR4 (HGNC:11850): (toll like receptor 4) 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 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. In silico studies have found a particularly strong binding of surface TLR4 with the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease-2019 (COVID-19). This receptor has also been implicated in signal transduction events induced by lipopolysaccharide (LPS) found in most gram-negative bacteria. Mutations in this gene have been associated with differences in LPS responsiveness, and with susceptibility to age-related macular degeneration. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2020]

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12816092).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TLR4	NM_138554.5	c.6G>A	p.Met2Ile	missense_variant	Exon 1 of 3	ENST00000355622.8	NP_612564.1
TLR4	NM_003266.4	c.-235G>A		5_prime_UTR_variant	Exon 1 of 4		NP_003257.1
TLR4	NM_138557.3	c.-428G>A		5_prime_UTR_variant	Exon 1 of 2		NP_612567.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TLR4	ENST00000355622.8	c.6G>A	p.Met2Ile	missense_variant	Exon 1 of 3	1	NM_138554.5	ENSP00000363089.5
ENSG00000285082	ENST00000697666.1	c.-235G>A		5_prime_UTR_variant	Exon 1 of 5			ENSP00000513391.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	8.7
DANN	Benign	0.78
DEOGEN2	Benign	0.13	.;.;T;T
Eigen	Benign	-0.81
Eigen_PC	Benign	-0.80
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.47	T;T;.;T
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.13	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.3	.;.;L;L
PhyloP100		0.12
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-0.49	.;.;.;N
REVEL	Benign	0.15
Sift	Benign	0.24	.;.;.;T
Sift4G	Benign	0.11	.;.;.;T
Polyphen		0.0	.;.;B;B
Vest4		0.27
MutPred		0.42		Gain of catalytic residue at L7 (P = 0.045);Gain of catalytic residue at L7 (P = 0.045);Gain of catalytic residue at L7 (P = 0.045);Gain of catalytic residue at L7 (P = 0.045);
MVP		0.52
MPC		0.094
ClinPred		0.13	T
GERP RS		2.2
PromoterAI		-0.083	Neutral
Varity_R		0.16
gMVP		0.52
Mutation Taster		=93/7	polymorphism

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: rs1005484206; hg19: chr9-120466756;