NM_138927.4(SON):c.5753_5756del (p.Val1918fs) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 21, 2016
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:: RCV000491471.3

Allele description [Variation Report for NM_138927.4(SON):c.5753_5756del (p.Val1918fs)]

NM_138927.4(SON):c.5753_5756del (p.Val1918fs)

Gene:

SON:SON DNA and RNA binding protein [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

21q22.11

Genomic location:

Preferred name:

NM_138927.4(SON):c.5753_5756del (p.Val1918fs)

Other names:

p.V1918Efs*87; NM_138927.4(SON):c.5753_5756del; p.Val1918fs

HGVS:

NC_000021.9:g.33554984_33554987del
NG_052981.1:g.16947_16950del
NM_001291411.2:c.5753_5756del
NM_001291412.3:c.245-2172_245-2169del
NM_032195.3:c.5753_5756del
NM_138927.4:c.5753_5756delMANE SELECT
NP_001278340.2:p.Val1918fs
NP_115571.3:p.Val1918fs
NP_620305.3:p.Val1918fs
NC_000021.8:g.34927288_34927291del
NC_000021.8:g.34927290_34927293del
NM_032195.2:c.5753_5756del
NM_032195.2:c.5753_5756delTTAG
NM_138927.1:c.5753_5756delTTAG
NM_138927.2:c.5751_5754delAGTT
NM_138927.2:c.5753_5756delTTAG
NM_138927.3:c.5753_5756del
NM_138927.4:c.5751_5754delMANE SELECT
NM_138927.4:c.5753_5756del
NR_103797.2:n.5808_5811del

Protein change:

V1918fs

Links:

OMIM: 182465.0001; dbSNP: rs886039773

NCBI 1000 Genomes Browser:

rs886039773

Molecular consequence:

NM_001291411.2:c.5753_5756del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032195.3:c.5753_5756del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_138927.4:c.5753_5756del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291412.3:c.245-2172_245-2169del - intron variant - [Sequence Ontology: SO:0001627]
NR_103797.2:n.5808_5811del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Global developmental delay (DD)
Identifiers:: MedGen: C0557874; Human Phenotype Ontology: HP:0001263

Name:: Failure to thrive
Synonyms:: Pediatric failure to thrive
Identifiers:: MedGen: C2315100; Human Phenotype Ontology: HP:0001508

Recent activity

Clear Turn Off Turn On

Riemerella anatipestifer strain 24RAST91 24_scaffold33, whole genome shotgun seq...
Riemerella anatipestifer strain 24RAST91 24_scaffold33, whole genome shotgun sequence
gi|2578734443|ref|NZ_JAVKXE01000003 gnl|WGS:NZ_JAVKXE01|24_scaffold33

Nucleotide
Riemerella anatipestifer strain RCAD1082 110_scaffolds_0, whole genome shotgun s...
Riemerella anatipestifer strain RCAD1082 110_scaffolds_0, whole genome shotgun sequence
gi|2713350705|ref|NZ_JAFELQ01000000 gnl|WGS:NZ_JAFELQ01|110_scaffolds_0

Nucleotide
Riemerella anatipestifer strain 11RAST10 11_scaffold1, whole genome shotgun sequ...
Riemerella anatipestifer strain 11RAST10 11_scaffold1, whole genome shotgun sequence
gi|2579104075|ref|NZ_JAVKVQ01000000 gnl|WGS:NZ_JAVKVQ01|11_scaffold1

Nucleotide
Plant sample from Ctenolophon englerianus
Plant sample from Ctenolophon englerianus

biosample
teneurin-3 isoform X11 [Rattus norvegicus]
teneurin-3 isoform X11 [Rattus norvegicus]
gi|2678903182|ref|XP_063131493.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000297721	Baylor Genetics - SON	criteria provided, single submitter (Submitter's publication)	Likely pathogenic (Jun 21, 2016)	de novo	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

SCV000297721

Baylor Genetics - SON

criteria provided, single submitter

(Submitter's publication)

Likely pathogenic
(Jun 21, 2016)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive.

Tokita MJ, Braxton AA, Shao Y, Lewis AM, Vincent M, Küry S, Besnard T, Isidor B, Latypova X, Bézieau S, Liu P, Motter CS, Melver CW, Robin NH, Infante EM, McGuire M, El-Gharbawy A, Littlejohn RO, McLean SD, Bi W, Bacino CA, Lalani SR, et al.

Am J Hum Genet. 2016 Sep 1;99(3):720-727. doi: 10.1016/j.ajhg.2016.06.035. Epub 2016 Aug 18.

PubMed [citation]

PMID:: 27545676
PMCID:: PMC5011061

Details of each submission

From Baylor Genetics - SON, SCV000297721.1

#	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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine