Submissions for variant NM_001378615.1(CC2D2A):c.3046G>A (p.Glu1016Lys)

gnomAD frequency: 0.00053  dbSNP: rs373960465

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV001087622	SCV000254668	likely benign	Familial aplasia of the vermis; Meckel-Gruber syndrome	2023-12-30	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000344416	SCV000345696	uncertain significance	not provided	2018-02-22	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000350715	SCV000447879	uncertain significance	Joubert syndrome 9	2018-01-13	criteria provided, single submitter	clinical testing	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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina	RCV000405623	SCV000447880	uncertain significance	Meckel syndrome, type 6	2018-01-13	criteria provided, single submitter	clinical testing	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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx	RCV000344416	SCV002013806	uncertain significance	not provided	2021-08-13	criteria provided, single submitter	clinical testing	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
New York Genome Center	RCV002227457	SCV002506784	uncertain significance	Meckel syndrome, type 6; Joubert syndrome 9; COACH syndrome 2	2021-05-14	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000350715	SCV003836407	uncertain significance	Joubert syndrome 9	2022-08-08	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000344416	SCV004701195	uncertain significance	not provided	2023-12-01	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004530191	SCV004743968	likely benign	CC2D2A-related disorder	2022-10-17	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).