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NC_000009.11:g.(?_139981452)_(140003043_?)del AND Rafiq syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 25, 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:
RCV004582012.2

Allele description [Variation Report for NC_000009.11:g.(?_139981452)_(140003043_?)del]

NC_000009.11:g.(?_139981452)_(140003043_?)del

Gene:
MAN1B1:mannosidase alpha class 1B member 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.3
Genomic location:
Chr9: 139981452 - 140003043 (on Assembly GRCh37)
Preferred name:
NC_000009.11:g.(?_139981452)_(140003043_?)del
HGVS:
NC_000009.11:g.(?_139981452)_(140003043_?)del

Condition(s)

Name:
Rafiq syndrome (RAFQS)
Identifiers:
MONDO: MONDO:0013624; MedGen: C3280127; Orphanet: 88616; OMIM: 614202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005067357Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 25, 2024) 		unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Diagnostic serum glycosylation profile in patients with intellectual disability as a result of MAN1B1 deficiency.

Van Scherpenzeel M, Timal S, Rymen D, Hoischen A, Wuhrer M, Hipgrave-Ederveen A, Grunewald S, Peanne R, Saada A, Edvardson S, Grønborg S, Ruijter G, Kattentidt-Mouravieva A, Brum JM, Freckmann ML, Tomkins S, Jalan A, Prochazkova D, Ondruskova N, Hansikova H, Willemsen MA, Hensbergen PJ, et al.

Brain. 2014 Apr;137(Pt 4):1030-8. doi: 10.1093/brain/awu019. Epub 2014 Feb 24.

PubMed [citation]
PMID:
24566669

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, SCV005067357.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the MAN1B1 gene has been identified. Loss-of-function variants in MAN1B1 are known to be pathogenic (PMID: 24566669). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with MAN1B1-related conditions. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024