NM_020070.4(IGLL1):c.420T>C (p.Phe140=) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Apr 1, 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:: RCV000757400.25

Allele description [Variation Report for NM_020070.4(IGLL1):c.420T>C (p.Phe140=)]

NM_020070.4(IGLL1):c.420T>C (p.Phe140=)

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.420T>C (p.Phe140=)

HGVS:

NC_000022.11:g.23573488A>G
NG_009791.1:g.11821T>C
NM_001369906.1:c.423T>C
NM_020070.4:c.420T>CMANE SELECT
NM_152855.3:c.*49T>C
NP_001356835.1:p.Phe141=
NP_064455.1:p.Phe140=
LRG_69:g.11821T>C
NC_000022.10:g.23915675A>G
NM_020070.3:c.420T>C
p.Phe140Phe

Links:

dbSNP: rs1064423

NCBI 1000 Genomes Browser:

rs1064423

Molecular consequence:

NM_152855.3:c.*49T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001369906.1:c.423T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_020070.4:c.420T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000885604	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Apr 1, 2018)	germline	clinical testing	Citation Link,
SCV001746440	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Apr 1, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000885604

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(Apr 1, 2018)

germline

clinical testing

Citation Link,

SCV001746440

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Apr 1, 2021)

germline

clinical testing

Citation Link

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
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885604.1

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

Description

The c.420T>C; p.Phe140Phe variant (rs1064423) does not alter the amino acid sequence of the IGLL1 protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in association with antibody deficiency in medical literature or in gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.04% (identified on 106 out of 276,448 chromosomes). Based on the available information, the c.420T>C variant is likely to be benign.

#	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 CeGaT Center for Human Genetics Tuebingen, SCV001746440.14

#	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	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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