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NM_015915.5(ATL1):c.1173C>T (p.His391=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 22, 2020
Accession:
VCV000313305.14
Variation ID:
313305
Description:
single nucleotide variant
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NM_015915.5(ATL1):c.1173C>T (p.His391=)

Allele ID
337987
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q22.1
Genomic location
14: 50628084 (GRCh38) GRCh38 UCSC
14: 51094802 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000014.9:g.50628084C>T
NG_009028.1:g.100003C>T
NM_001127713.1:c.1173C>T NP_001121185.1:p.His391= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000014.9:50628083:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00012
The Genome Aggregation Database (gnomAD) 0.00013
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00012
Trans-Omics for Precision Medicine (TOPMed) 0.00011
Links
ClinGen: CA7180450
dbSNP: rs149340140
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 3, 2020 RCV001086937.3
Benign 1 criteria provided, single submitter Dec 30, 2016 RCV000518429.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 22, 2020 RCV000487834.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATL1 - - GRCh38
GRCh37
281 310

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 30, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612427.1
Submitted: (Aug 17, 2017)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000386896.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Nov 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000574974.12
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary spastic paraplegia 3A
Allele origin: germline
Invitae
Accession: SCV001002601.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Dec 22, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000983776.2
Submitted: (Sep 23, 2021)
Evidence details

Functional evidence

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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

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs149340140...

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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 Dec 04, 2021