Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_173630.4(RTTN):c.6445G>A (p.Ala2149Thr)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Sep 23, 2021)
Last evaluated:
Oct 20, 2020
Accession:
VCV000130194.8
Variation ID:
130194
Description:
single nucleotide variant
Help

NM_173630.4(RTTN):c.6445G>A (p.Ala2149Thr)

Allele ID
135641
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
18q22.2
Genomic location
18: 70006461 (GRCh38) GRCh38 UCSC
18: 67673697 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000018.10:g.70006461C>T
NC_000018.9:g.67673697C>T
NG_033104.1:g.204266G>A
... more HGVS
Protein change
A2149T, A1237T
Other names
-
Canonical SPDI
NC_000018.10:70006460:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00300 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00582
1000 Genomes Project 0.00300
Exome Aggregation Consortium (ExAC) 0.00574
The Genome Aggregation Database (gnomAD) 0.00723
Trans-Omics for Precision Medicine (TOPMed) 0.00491
The Genome Aggregation Database (gnomAD), exomes 0.00577
Links
ClinGen: CA155028
dbSNP: rs34989098
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Oct 20, 2020 RCV000224256.7
Likely benign 1 criteria provided, single submitter May 5, 2015 RCV000118223.4
Uncertain significance 1 criteria provided, single submitter Sep 1, 2017 RCV000679856.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
RTTN - - GRCh38
GRCh37
411 542

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Sep 01, 2017)
criteria provided, single submitter
Method: clinical testing
Microcephaly, short stature, and polymicrogyria with or without seizures
(Autosomal recessive inheritance)
Allele origin: germline
Baylor Genetics
Accession: SCV000807206.1
Submitted: (Oct 16, 2017)
Evidence details
Publications
PubMed (1)
Comment:
Possible pathogenicity based on finding it once in our laboratory in trans with another missense variant in a 3-year-old female with microcephaly, craniosynostosis, dysmorphisms, fused … (more)
Likely benign
(Oct 20, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000526492.5
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(May 05, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000152582.2
Submitted: (Sep 15, 2015)
Evidence details
Likely Benign
(Oct 07, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281393.1
Submitted: (May 19, 2016)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001105284.2
Submitted: (Jan 29, 2020)
Evidence details
Likely benign
(Jul 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001501206.3
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Molecular findings among patients referred for clinical whole-exome sequencing. Yang Y JAMA 2014 PMID: 25326635

Text-mined citations for rs34989098...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021