NM_007315.4(STAT1):c.1992G>C (p.Leu664=) AND multiple conditions

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

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jul 19, 2022
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:: RCV002079678.5

Allele description

NM_007315.4(STAT1):c.1992G>C (p.Leu664=)

Gene:

STAT1:signal transducer and activator of transcription 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q32.2

Genomic location:

Preferred name:

NM_007315.4(STAT1):c.1992G>C (p.Leu664=)

HGVS:

NC_000002.12:g.190976907C>G
NG_008294.1:g.42344G>C
NM_001384880.1:c.1932G>C
NM_001384881.1:c.1998G>C
NM_001384882.1:c.1986G>C
NM_001384883.1:c.1893G>C
NM_001384884.1:c.1962+36G>C
NM_001384885.1:c.1833G>C
NM_001384886.1:c.1992G>C
NM_001384887.1:c.1899G>C
NM_001384888.1:c.1962G>C
NM_001384889.1:c.1992G>C
NM_001384890.1:c.1902G>C
NM_001384891.1:c.2028G>C
NM_007315.4:c.1992G>CMANE SELECT
NM_139266.3:c.1992G>C
NP_001371809.1:p.Leu644=
NP_001371810.1:p.Leu666=
NP_001371811.1:p.Leu662=
NP_001371812.1:p.Leu631=
NP_001371814.1:p.Leu611=
NP_001371815.1:p.Leu664=
NP_001371816.1:p.Leu633=
NP_001371817.1:p.Leu654=
NP_001371818.1:p.Leu664=
NP_001371819.1:p.Leu634=
NP_001371820.1:p.Leu676=
NP_009330.1:p.Leu664=
NP_644671.1:p.Leu664=
LRG_111:g.42344G>C
NC_000002.11:g.191841633C>G

Links:

dbSNP: rs1691949058

NCBI 1000 Genomes Browser:

rs1691949058

Molecular consequence:

NM_001384884.1:c.1962+36G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001384880.1:c.1932G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384881.1:c.1998G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384882.1:c.1986G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384883.1:c.1893G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384885.1:c.1833G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384886.1:c.1992G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384887.1:c.1899G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384888.1:c.1962G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384889.1:c.1992G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384890.1:c.1902G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001384891.1:c.2028G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_007315.4:c.1992G>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_139266.3:c.1992G>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Immunodeficiency 31B
Synonyms:: STAT1 DEFICIENCY, AUTOSOMAL RECESSIVE; Mycobacterial and viral infections, susceptibility to, autosomal recessive; IMMUNODEFICIENCY 31B, MYCOBACTERIAL AND VIRAL INFECTIONS, AUTOSOMAL RECESSIVE
Identifiers:: MONDO: MONDO:0013427; MedGen: C3151088; OMIM: 613796

Name:: Autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome
Synonyms:: Candidiasis, familial, 7; Immunodeficiency 31C
Identifiers:: MONDO: MONDO:0013599; MedGen: C3279990; Orphanet: 391487; OMIM: 614162

Name:: Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency
Synonyms:: IMMUNODEFICIENCY 31A, MYCOBACTERIOSIS, AUTOSOMAL DOMINANT; STAT1 DEFICIENCY, AUTOSOMAL DOMINANT; Immunodeficiency 31a
Identifiers:: MONDO: MONDO:0013956; MedGen: C4013950; Orphanet: 319595; OMIM: 614892

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002427584	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jul 19, 2022)	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

SCV002427584

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jul 19, 2022)

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 Invitae, SCV002427584.3

#	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: Feb 28, 2024

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