NM_014989.7(RIMS1):c.5053A>G (p.Thr1685Ala) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jan 4, 2024
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:: RCV001036748.8

Allele description [Variation Report for NM_014989.7(RIMS1):c.5053A>G (p.Thr1685Ala)]

NM_014989.7(RIMS1):c.5053A>G (p.Thr1685Ala)

Gene:

RIMS1:regulating synaptic membrane exocytosis 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q13

Genomic location:

Preferred name:

NM_014989.7(RIMS1):c.5053A>G (p.Thr1685Ala)

HGVS:

NC_000006.12:g.72400688A>G
NG_016209.1:g.518741A>G
NM_001168407.2:c.3013A>G
NM_001168408.2:c.2428A>G
NM_001168409.2:c.2257A>G
NM_001168410.2:c.2455A>G
NM_001168411.2:c.634A>G
NM_001350414.2:c.2974A>G
NM_001350415.2:c.3070A>G
NM_001350416.2:c.3019A>G
NM_001350417.2:c.2500A>G
NM_001350418.2:c.2992A>G
NM_001350419.2:c.2272A>G
NM_001350420.2:c.3127A>G
NM_001350421.2:c.2872A>G
NM_001350422.2:c.2497A>G
NM_001350423.2:c.2761A>G
NM_001350424.2:c.2359A>G
NM_001350425.2:c.2971A>G
NM_001350426.2:c.2347A>G
NM_001350427.2:c.2425A>G
NM_001350428.2:c.2431A>G
NM_001350429.2:c.2791A>G
NM_001350430.2:c.2428A>G
NM_001350431.2:c.3109A>G
NM_001350432.2:c.2335A>G
NM_001350433.2:c.3100A>G
NM_001350434.2:c.2575A>G
NM_001350435.2:c.2962A>G
NM_001350436.2:c.3205A>G
NM_001350437.2:c.2956A>G
NM_001350438.2:c.2680A>G
NM_001350439.2:c.2944A>G
NM_001350440.2:c.2344A>G
NM_001350441.2:c.2941A>G
NM_001350442.2:c.2683A>G
NM_001350443.2:c.2914A>G
NM_001350444.2:c.2788A>G
NM_001350445.2:c.2581A>G
NM_001350446.2:c.3199A>G
NM_001350447.2:c.2860A>G
NM_001350448.2:c.3016A>G
NM_001350449.2:c.2407A>G
NM_001350450.2:c.2356A>G
NM_001350454.2:c.2923A>G
NM_001350455.2:c.2275A>G
NM_001350456.2:c.3196A>G
NM_001350457.2:c.2953A>G
NM_001350458.2:c.3022A>G
NM_001350459.2:c.2875A>G
NM_001350460.2:c.2893A>G
NM_001350461.2:c.2743A>G
NM_001350462.2:c.3058A>G
NM_001350463.2:c.2698A>G
NM_001350464.2:c.2701A>G
NM_001350465.2:c.2185A>G
NM_001350466.2:c.2704A>G
NM_001350467.2:c.2620A>G
NM_001350468.2:c.2545A>G
NM_001350469.2:c.2773A>G
NM_001350470.2:c.2461A>G
NM_001350471.2:c.2854A>G
NM_001350472.2:c.2380A>G
NM_001350473.2:c.2383A>G
NM_001350474.2:c.2746A>G
NM_014989.7:c.5053A>GMANE SELECT
NP_001161879.1:p.Thr1005Ala
NP_001161880.1:p.Thr810Ala
NP_001161881.1:p.Thr753Ala
NP_001161882.1:p.Thr819Ala
NP_001161883.1:p.Thr212Ala
NP_001337343.1:p.Thr992Ala
NP_001337344.1:p.Thr1024Ala
NP_001337345.1:p.Thr1007Ala
NP_001337346.1:p.Thr834Ala
NP_001337347.1:p.Thr998Ala
NP_001337348.1:p.Thr758Ala
NP_001337349.1:p.Thr1043Ala
NP_001337350.1:p.Thr958Ala
NP_001337351.1:p.Thr833Ala
NP_001337352.1:p.Thr921Ala
NP_001337353.1:p.Thr787Ala
NP_001337354.1:p.Thr991Ala
NP_001337355.1:p.Thr783Ala
NP_001337356.1:p.Thr809Ala
NP_001337357.1:p.Thr811Ala
NP_001337358.1:p.Thr931Ala
NP_001337359.1:p.Thr810Ala
NP_001337360.1:p.Thr1037Ala
NP_001337361.1:p.Thr779Ala
NP_001337362.1:p.Thr1034Ala
NP_001337363.1:p.Thr859Ala
NP_001337364.1:p.Thr988Ala
NP_001337365.1:p.Thr1069Ala
NP_001337366.1:p.Thr986Ala
NP_001337367.1:p.Thr894Ala
NP_001337368.1:p.Thr982Ala
NP_001337369.1:p.Thr782Ala
NP_001337370.1:p.Thr981Ala
NP_001337371.1:p.Thr895Ala
NP_001337372.1:p.Thr972Ala
NP_001337373.1:p.Thr930Ala
NP_001337374.1:p.Thr861Ala
NP_001337375.1:p.Thr1067Ala
NP_001337376.1:p.Thr954Ala
NP_001337377.1:p.Thr1006Ala
NP_001337378.1:p.Thr803Ala
NP_001337379.1:p.Thr786Ala
NP_001337383.1:p.Thr975Ala
NP_001337384.1:p.Thr759Ala
NP_001337385.1:p.Thr1066Ala
NP_001337386.1:p.Thr985Ala
NP_001337387.1:p.Thr1008Ala
NP_001337388.1:p.Thr959Ala
NP_001337389.1:p.Thr965Ala
NP_001337390.1:p.Thr915Ala
NP_001337391.1:p.Thr1020Ala
NP_001337392.1:p.Thr900Ala
NP_001337393.1:p.Thr901Ala
NP_001337394.1:p.Thr729Ala
NP_001337395.1:p.Thr902Ala
NP_001337396.1:p.Thr874Ala
NP_001337397.1:p.Thr849Ala
NP_001337398.1:p.Thr925Ala
NP_001337399.1:p.Thr821Ala
NP_001337400.1:p.Thr952Ala
NP_001337401.1:p.Thr794Ala
NP_001337402.1:p.Thr795Ala
NP_001337403.1:p.Thr916Ala
NP_055804.2:p.Thr1685Ala
NP_055804.2:p.Thr1685Ala
NC_000006.11:g.73110390A>G
NM_014989.5:c.5053A>G

Protein change:

T1005A

Links:

dbSNP: rs200035429

NCBI 1000 Genomes Browser:

rs200035429

Molecular consequence:

NM_001168407.2:c.3013A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001168408.2:c.2428A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001168409.2:c.2257A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001168410.2:c.2455A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001168411.2:c.634A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350414.2:c.2974A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350415.2:c.3070A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350416.2:c.3019A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350417.2:c.2500A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350418.2:c.2992A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350419.2:c.2272A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350420.2:c.3127A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350421.2:c.2872A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350422.2:c.2497A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350423.2:c.2761A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350424.2:c.2359A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350425.2:c.2971A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350426.2:c.2347A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350427.2:c.2425A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350428.2:c.2431A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350429.2:c.2791A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350430.2:c.2428A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350431.2:c.3109A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350432.2:c.2335A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350433.2:c.3100A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350434.2:c.2575A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350435.2:c.2962A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350436.2:c.3205A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350437.2:c.2956A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350438.2:c.2680A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350439.2:c.2944A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350440.2:c.2344A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350441.2:c.2941A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350442.2:c.2683A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350443.2:c.2914A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350444.2:c.2788A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350445.2:c.2581A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350446.2:c.3199A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350447.2:c.2860A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350448.2:c.3016A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350449.2:c.2407A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350450.2:c.2356A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350454.2:c.2923A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350455.2:c.2275A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350456.2:c.3196A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350457.2:c.2953A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350458.2:c.3022A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350459.2:c.2875A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350460.2:c.2893A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350461.2:c.2743A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350462.2:c.3058A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350463.2:c.2698A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350464.2:c.2701A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350465.2:c.2185A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350466.2:c.2704A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350467.2:c.2620A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350468.2:c.2545A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350469.2:c.2773A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350470.2:c.2461A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350471.2:c.2854A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350472.2:c.2380A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350473.2:c.2383A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001350474.2:c.2746A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014989.7:c.5053A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001200126	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 4, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001749863	GenomeConnect - Invitae Patient Insights Network	no classification provided	not provided	unknown	phenotyping only

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001200126

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 4, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001749863

GenomeConnect - Invitae Patient Insights Network

no classification provided

not provided

unknown

phenotyping only

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	phenotyping only

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001200126.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 1685 of the RIMS1 protein (p.Thr1685Ala). This variant is present in population databases (rs200035429, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with RIMS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 835781). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

From GenomeConnect - Invitae Patient Insights Network, SCV001749863.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	phenotyping only	not provided

Description

Variant interpreted as Uncertain significance and reported on 01-24-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine