NC_000006.12:g.99593111G>C AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001268365.13

Allele description [Variation Report for NC_000006.12:g.99593111G>C]

NC_000006.12:g.99593111G>C

Genes:

PRDM13:PR/SET domain 13 [Gene - OMIM - HGNC]
LOC111365204:CCNC and PRDM13 intergenic region DNase I hypersensitve site DHS6S1 [Gene - OMIM]

Variant type:

single nucleotide variant

Cytogenetic location:

6q16.2

Genomic location:

Preferred name:

NC_000006.12:g.99593111G>C

HGVS:

NC_000006.12:g.99593111G>C
NG_055818.1:g.327G>C
NC_000006.11:g.100040987G>C

Nucleotide change:

CHR6:100,040,987, G-C

Links:

OMIM: 616842.0002; dbSNP: rs1554264613

NCBI 1000 Genomes Browser:

rs1554264613

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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dynein light chain Tctex-type 3 [Rattus norvegicus]
dynein light chain Tctex-type 3 [Rattus norvegicus]
gi|61557355|ref|NP_001013246.1|

Protein
CCND2 [Echinops telfairi]
CCND2 [Echinops telfairi]
Gene ID:101657079

Gene
Nlgn3 neuroligin 3 [Mus musculus]
Nlgn3 neuroligin 3 [Mus musculus]
Gene ID:245537

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001447240	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001588211	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 18, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 26507665, 27551809, 31043363, 31814698, 28492532
SCV005041084	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Jul 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001447240

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 23, 2020)

germline

clinical testing

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

SCV001588211

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 18, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV005041084

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Jul 1, 2024)

germline

clinical testing

Citation Link

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	germline	yes	2	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

North Carolina Macular Dystrophy Is Caused by Dysregulation of the Retinal Transcription Factor PRDM13.

Small KW, DeLuca AP, Whitmore SS, Rosenberg T, Silva-Garcia R, Udar N, Puech B, Garcia CA, Rice TA, Fishman GA, Héon E, Folk JC, Streb LM, Haas CM, Wiley LA, Scheetz TE, Fingert JH, Mullins RF, Tucker BA, Stone EM.

Ophthalmology. 2016 Jan;123(1):9-18. doi: 10.1016/j.ophtha.2015.10.006. Epub 2015 Oct 24.

PubMed [citation]

PMID:: 26507665
PMCID:: PMC4695238

See all PubMed Citations (6)

Details of each submission

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447240.2

#	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	germline	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001588211.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant occurs in a non-coding region of the PRDM13 gene. It does not change the encoded amino acid sequence of the PRDM13 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with North Carolina macular dystrophy (PMID: 26507665, 27551809, 31043363, 31814698). It has also been observed to segregate with disease in related individuals. This variant is also known as V2 or chromosome 6: 99,593,111 (G>C) NC_000006.11(GRCh38):g.100040987G>C. For these reasons, this variant has been classified as Pathogenic.

#	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 CeGaT Center for Human Genetics Tuebingen, SCV005041084.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

Description

PRDM13: PP1:Strong, PM1, PM2, PS4:Moderate

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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