NM_002468.5(MYD88):c.103_104del (p.Leu35fs) AND Pyogenic bacterial infections due to MyD88 deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Nov 29, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001780440.4

Allele description

NM_002468.5(MYD88):c.103_104del (p.Leu35fs)

Gene:

MYD88:MYD88 innate immune signal transduction adaptor [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_002468.5(MYD88):c.103_104del (p.Leu35fs)

HGVS:

NC_000003.12:g.38138801CT[1]
NG_016964.1:g.5324CT[1]
NG_023225.1:g.3440GA[1]
NM_001172566.2:c.103_104del
NM_001172567.2:c.103_104del
NM_001172568.2:c.103_104del
NM_001172569.3:c.103_104del
NM_001365876.1:c.103_104del
NM_001365877.1:c.103_104del
NM_001374787.1:c.103_104del
NM_002468.5:c.103_104delMANE SELECT
NP_001166037.2:p.Leu35fs
NP_001166038.2:p.Leu35fs
NP_001166039.2:p.Leu35fs
NP_001166040.2:p.Leu35fs
NP_001352805.1:p.Leu35fs
NP_001352806.1:p.Leu35fs
NP_001361716.1:p.Leu35fs
NP_002459.3:p.Leu35fs
LRG_157t1:c.142_143del
LRG_157:g.5324CT[1]
NC_000003.11:g.38180291_38180292del
NC_000003.11:g.38180292CT[1]
NM_001172567.1:c.142_143del
NM_002468.4:c.142_143del

Protein change:

L35fs

Links:

dbSNP: rs776336832

NCBI 1000 Genomes Browser:

rs776336832

Molecular consequence:

NM_001172566.2:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172567.2:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172568.2:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172569.3:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365876.1:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001365877.1:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374787.1:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002468.5:c.103_104del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Pyogenic bacterial infections due to MyD88 deficiency (IMD68)
Synonyms:: PYOGENIC BACTERIAL INFECTIONS, RECURRENT, DUE TO MYD88 DEFICIENCY; Myd88 deficiency
Identifiers:: MONDO: MONDO:0012839; MedGen: C2677092; Orphanet: 183713; OMIM: 612260

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002025624	New York Genome Center - CSER-NYCKidSeq	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Likely pathogenic (May 31, 2020)	inherited	clinical testing	Citation Link,
SCV002198359	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 29, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18669862, 20538326, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002025624

New York Genome Center - CSER-NYCKidSeq

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Likely pathogenic
(May 31, 2020)

inherited

clinical testing

Citation Link,

SCV002198359

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 29, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	unknown	1	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Pyogenic bacterial infections in humans with MyD88 deficiency.

von Bernuth H, Picard C, Jin Z, Pankla R, Xiao H, Ku CL, Chrabieh M, Mustapha IB, Ghandil P, Camcioglu Y, Vasconcelos J, Sirvent N, Guedes M, Vitor AB, Herrero-Mata MJ, Aróstegui JI, Rodrigo C, Alsina L, Ruiz-Ortiz E, Juan M, Fortuny C, Yagüe J, et al.

Science. 2008 Aug 1;321(5889):691-6. doi: 10.1126/science.1158298.

PubMed [citation]

PMID:: 18669862
PMCID:: PMC2688396

Myeloid differentiation primary response gene 88 (MyD88) deficiency in a large kindred.

Conway DH, Dara J, Bagashev A, Sullivan KE.

J Allergy Clin Immunol. 2010 Jul;126(1):172-5. doi: 10.1016/j.jaci.2010.04.014. Epub 2010 Jun 9. No abstract available.

PubMed [citation]

PMID:: 20538326

See all PubMed Citations (3)

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002025624.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	unknown	1	not provided	not provided		1	not provided	not provided	not provided

From Invitae, SCV002198359.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Leu48Valfs*22) in the MYD88 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MYD88 are known to be pathogenic (PMID: 18669862, 20538326). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1316463). This variant has not been reported in the literature in individuals affected with MYD88-related conditions. This variant is present in population databases (rs776336832, gnomAD 0.004%).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 14, 2024

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