NM_001167.4(XIAP):c.-10_977+11del AND Lymphoproliferative syndrome 2

Germline classification:: Pathogenic (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001250232.1

Allele description [Variation Report for NM_001167.4(XIAP):c.-10_977+11del]

NM_001167.4(XIAP):c.-10_977+11del

Gene:

XIAP:X-linked inhibitor of apoptosis [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq25

Genomic location:

Preferred name:

NM_001167.4(XIAP):c.-10_977+11del

HGVS:

NC_000023.11:g.123885652_123888728del
NC_000023.11:g.123885653_123888729del
NG_007264.1:g.30456_33532del
NM_001167.4:c.-10_977+11delMANE SELECT
NM_001204401.2:c.-10_977+11del
NM_001378590.1:c.-10_977+11del
NM_001378591.1:c.-10_977+11del
NM_001378592.1:c.-10_977+11del
LRG_19:g.30456_33532del
NC_000023.10:g.123019502_123022578del
NC_000023.10:g.123019503_123022579del

Molecular consequence:

NM_001167.4:c.-10_977+11del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001204401.2:c.-10_977+11del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001378590.1:c.-10_977+11del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001378591.1:c.-10_977+11del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001378592.1:c.-10_977+11del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001167.4:c.-10_977+11del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001204401.2:c.-10_977+11del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001378590.1:c.-10_977+11del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001378591.1:c.-10_977+11del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001378592.1:c.-10_977+11del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001167.4:c.-10_977+11del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001204401.2:c.-10_977+11del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001378590.1:c.-10_977+11del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001378591.1:c.-10_977+11del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001378592.1:c.-10_977+11del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Lymphoproliferative syndrome 2 (LPFS2)
Synonyms:: CD27 DEFICIENCY; Combined immunodeficiency due to CD27 deficiency
Identifiers:: MONDO: MONDO:0014054; MedGen: C3554540; Orphanet: 238505; OMIM: 615122

Recent activity

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PREDICTED: Danio rerio ankyrin repeat and EF-hand domain containing 1a (ankef1a)...
PREDICTED: Danio rerio ankyrin repeat and EF-hand domain containing 1a (ankef1a), transcript variant X1, mRNA
gi|2800567175|ref|XM_005160755.5|

Nucleotide
Danio rerio ankyrin repeat and EF-hand domain containing 1a (ankef1a), mRNA
Danio rerio ankyrin repeat and EF-hand domain containing 1a (ankef1a), mRNA
gi|70887734|ref|NM_001025543.1|

Nucleotide
Murina rongjiangensis voucher GZHU 15375 cytochrome oxidase subunit 1 (COI) gene...
Murina rongjiangensis voucher GZHU 15375 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|1789824099|gb|MN549083.1|

Nucleotide
Murina rongjiangensis voucher GZHU 15120 cytochrome oxidase subunit 1 (COI) gene...
Murina rongjiangensis voucher GZHU 15120 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
gi|1789824095|gb|MN549081.1|

Nucleotide
Bagre marinus
Bagre marinus
Bagre marinus population genetic

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001424513	Centogene AG - the Rare Disease Company	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	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

SCV001424513

Centogene AG - the Rare Disease Company

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Centogene AG - the Rare Disease Company, SCV001424513.2

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 29, 2024

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