GeneBe

rs1319438

Variant names:

Variant summary

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

The NM_001172567.2(MYD88):​c.101C>A​(p.Ser34Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

MYD88
NM_001172567.2 missense

Scores

3
10
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.55

Publications

4 publications found
Variant links:
Genes affected
MYD88 (HGNC:7562): (MYD88 innate immune signal transduction adaptor) This gene encodes a cytosolic adapter protein that plays a central role in the innate and adaptive immune response. This protein functions as an essential signal transducer in the interleukin-1 and Toll-like receptor signaling pathways. These pathways regulate that activation of numerous proinflammatory genes. The encoded protein consists of an N-terminal death domain and a C-terminal Toll-interleukin1 receptor domain. Patients with defects in this gene have an increased susceptibility to pyogenic bacterial infections. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010]
MYD88 Gene-Disease associations (from GenCC):
  • pyogenic bacterial infections due to MyD88 deficiency
    Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172567.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MYD88
NM_002468.5
MANE Select
c.101C>Ap.Ser34Tyr
missense
Exon 1 of 5NP_002459.3
MYD88
NM_001172567.2
c.101C>Ap.Ser34Tyr
missense
Exon 1 of 5NP_001166038.2
MYD88
NM_001172568.2
c.101C>Ap.Ser34Tyr
missense
Exon 1 of 4NP_001166039.2

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MYD88
ENST00000650905.2
MANE Select
c.101C>Ap.Ser34Tyr
missense
Exon 1 of 5ENSP00000498360.2
MYD88
ENST00000421516.3
TSL:1
c.101C>Ap.Ser34Tyr
missense
Exon 1 of 5ENSP00000391753.3
MYD88
ENST00000417037.8
TSL:1
c.101C>Ap.Ser34Tyr
missense
Exon 1 of 4ENSP00000401399.4

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.77
BayesDel_addAF
Benign
-0.035
T
BayesDel_noAF
Benign
-0.29
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.20
T
Eigen
Uncertain
0.30
Eigen_PC
Benign
0.20
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.94
D
M_CAP
Uncertain
0.28
D
MetaRNN
Uncertain
0.51
D
MetaSVM
Benign
-0.55
T
MutationAssessor
Uncertain
2.4
M
PhyloP100
2.6
PrimateAI
Pathogenic
0.80
T
PROVEAN
Uncertain
-4.2
D
REVEL
Uncertain
0.33
Sift
Uncertain
0.0090
D
Sift4G
Uncertain
0.0090
D
Polyphen
0.95
P
Vest4
0.37
MutPred
0.61
Gain of glycosylation at S34 (P = 0.0354)
MVP
0.54
MPC
1.5
ClinPred
0.99
D
GERP RS
2.4
PromoterAI
-0.0098
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.61
Mutation Taster
=68/32
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

Publications

Other links and lift over

dbSNP: rs1319438; hg19: chr3-38180292; API