NR_023317.1(RNU7-1):n.28C>G AND not provided

Germline classification:: Likely pathogenic (2 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:: RCV004598147.9

Allele description [Variation Report for NR_023317.1(RNU7-1):n.28C>G]

NR_023317.1(RNU7-1):n.28C>G

Genes:

RNU7-1:RNA, U7 small nuclear 1 [Gene - OMIM - HGNC]
C12orf57:chromosome 12 open reading frame 57 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NR_023317.1(RNU7-1):n.28C>G

HGVS:

NC_000012.12:g.6943843C>G
NG_008047.1:g.24381C>G
NG_008047.2:g.24386C>G
NG_034262.1:g.5027C>G
NG_125067.2:g.114C>G
NM_001301834.1:c.-16+181C>G
NM_001301836.2:c.13+181C>G
NM_001301837.1:c.-279C>G
NM_001301838.1:c.-480C>G
NM_138425.3:c.-279C>G
NC_000012.11:g.7053006C>G
NG_125067.1:g.114C>G
NR_023317.1:n.28C>G
NR_126035.1:n.27C>G

Links:

dbSNP: rs180837208

NCBI 1000 Genomes Browser:

rs180837208

Molecular consequence:

NM_001301834.1:c.-16+181C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001301836.2:c.13+181C>G - intron variant - [Sequence Ontology: SO:0001627]
NR_023317.1:n.28C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV005092545	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely pathogenic (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV005333357	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 29, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005092545

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Likely pathogenic
(Jul 1, 2024)

germline

clinical testing

Citation Link,

SCV005333357

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 29, 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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV005092545.9

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

Description

RNU7-1: PM3:Strong, PM2, PS1:Supporting

#	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		1	not provided	not provided	not provided

From GeneDx, SCV005333357.1

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

Description

Observed with a second RNU7-1 variant in a patient with nystagmus, microcephaly, and dystonia, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (PMID: 37171742); Published functional studies demonstrate severely impaired RNU7-1 function (PMID: 16547514); Also known as n.28C>G; This variant is associated with the following publications: (PMID: 16547514, 33230297, 37171742)

#	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		not provided	not provided	not provided	not provided

Last Updated: Jul 13, 2025

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