NM_015272.5(RPGRIP1L):c.2968CCT[2] (p.Pro992del) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 15, 2022
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:: RCV002542916.2

Allele description [Variation Report for NM_015272.5(RPGRIP1L):c.2968CCT[2] (p.Pro992del)]

NM_015272.5(RPGRIP1L):c.2968CCT[2] (p.Pro992del)

Gene:

RPGRIP1L:RPGRIP1 like [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16q12.2

Genomic location:

Preferred name:

NM_015272.5(RPGRIP1L):c.2968CCT[2] (p.Pro992del)

HGVS:

NC_000016.10:g.53638396GAG[2]
NG_008991.2:g.70458CCT[2]
NM_001127897.4:c.2959-548CCT[2]
NM_001308334.3:c.2968CCT[2]
NM_001330538.2:c.2959-548CCT[2]
NM_015272.5:c.2968CCT[2]MANE SELECT
NM_015272.5:c.2974_2976del
NP_001295263.1:p.Pro992del
NP_056087.2:p.Pro992del
LRG_696t1:c.2959-548CCT[2]
LRG_696t2:c.2968CCT[2]
LRG_696:g.70458CCT[2]
LRG_696p2:p.Pro992del
NC_000016.9:g.53672306_53672308del
NC_000016.9:g.53672308GAG[2]
NM_015272.4:c.2974_2976delCCT
NM_015272.5:c.2974_2976delMANE SELECT
NM_015272.5:c.2974_2976delCCTMANE SELECT

Protein change:

P992del

Links:

dbSNP: rs752076060

NCBI 1000 Genomes Browser:

rs752076060

Molecular consequence:

NM_001308334.3:c.2968CCT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_015272.5:c.2968CCT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127897.4:c.2959-548CCT[2] - intron variant - [Sequence Ontology: SO:0001627]
NM_001330538.2:c.2959-548CCT[2] - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Familial aplasia of the vermis
Synonyms:: CEREBELLOPARENCHYMAL DISORDER IV; Joubert syndrome; Cerebelloparenchymal disorder 4; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018772; MedGen: C0431399; Orphanet: 475; OMIM: PS213300

Name:: Meckel-Gruber syndrome
Synonyms:: DYSENCEPHALIA SPLANCHNOCYSTICA; Gruber syndrome; Dysencephalia splachnocystica
Identifiers:: MONDO: MONDO:0018921; MedGen: C0265215; OMIM: PS249000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003245759	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003245759

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 15, 2022)

germline

clinical testing

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

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

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, SCV003245759.1

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

Description

This variant, c.2974_2976del, results in the deletion of 1 amino acid(s) of the RPGRIP1L protein (p.Pro992del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs752076060, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with RPGRIP1L-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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

Last Updated: Nov 24, 2024

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