NM_020070.4(IGLL1):c.485T>A (p.Met162Lys) AND Agammaglobulinemia 2, autosomal recessive

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV000559039.19

Allele description [Variation Report for NM_020070.4(IGLL1):c.485T>A (p.Met162Lys)]

NM_020070.4(IGLL1):c.485T>A (p.Met162Lys)

Gene:

IGLL1:immunoglobulin lambda like polypeptide 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.23

Genomic location:

Preferred name:

NM_020070.4(IGLL1):c.485T>A (p.Met162Lys)

HGVS:

NC_000022.11:g.23573423A>T
NG_009791.1:g.11886T>A
NM_001369906.1:c.488T>A
NM_020070.4:c.485T>AMANE SELECT
NM_152855.3:c.*114T>A
NP_001356835.1:p.Met163Lys
NP_064455.1:p.Met162Lys
LRG_69:g.11886T>A
NC_000022.10:g.23915610A>T
NM_020070.3:c.485T>A

Protein change:

M162K

Links:

dbSNP: rs111903752

NCBI 1000 Genomes Browser:

rs111903752

Molecular consequence:

NM_152855.3:c.*114T>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001369906.1:c.488T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020070.4:c.485T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Agammaglobulinemia 2, autosomal recessive (AGM2)
Synonyms:: AGAMMAGLOBULINEMIA, AUTOSOMAL RECESSIVE, DUE TO IGLL1 DEFECT
Identifiers:: MONDO: MONDO:0013287; MedGen: C3150750; OMIM: 613500

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000604019	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Nov 22, 2023)	germline	clinical testing	Citation Link,
SCV000650068	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000604019

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Nov 22, 2023)

germline

clinical testing

Citation Link,

SCV000650068

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 31, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000604019.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV000650068.6

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

#	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: Aug 25, 2024

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