NM_176806.4(MOCS2):c.30_34del (p.Leu10fs) AND Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 31, 2020
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:: RCV001196957.4

Allele description [Variation Report for NM_176806.4(MOCS2):c.30_34del (p.Leu10fs)]

NM_176806.4(MOCS2):c.30_34del (p.Leu10fs)

Gene:

MOCS2:molybdenum cofactor synthesis 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

5q11.2

Genomic location:

Preferred name:

NM_176806.4(MOCS2):c.30_34del (p.Leu10fs)

HGVS:

NC_000005.10:g.53108628AATAC[1]
NG_008435.2:g.6132GTATT[1]
NM_004531.5:c.-163GTATT[1]MANE SELECT
NM_176806.4:c.30_34del
NP_789776.1:p.Leu10fs
NC_000005.9:g.52404458AATAC[1]
NM_176806.3:c.30_34delGTATT

Protein change:

L10fs

Links:

dbSNP: rs1741117263

NCBI 1000 Genomes Browser:

rs1741117263

Molecular consequence:

NM_004531.5:c.-163GTATT[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_176806.4:c.30_34del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B
Synonyms:: Molybdenum cofactor deficiency, complementation group B; Molybdenum cofactor deficiency B
Identifiers:: MONDO: MONDO:0009644; MedGen: C1854989; Orphanet: 833; OMIM: 252160

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001367591	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 31, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005044762	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	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

SCV001367591

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 31, 2020)

unknown

clinical testing

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

SCV005044762

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	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

Details of each submission

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001367591.2

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

Description

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2.

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

From Neuberg Centre For Genomic Medicine, NCGM, SCV005044762.2

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

Description

The frame shift c.30_34del p.Leu10PhefsTer6 variant in MOCS2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Leu10PhefsTer6 variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Likely Pathogenic. This variant causes a frameshift starting with codon Leucine 10, changes this amino acid to Phenylalanine residue, and creates a premature Stop codon at position 6 of the new reading frame, denoted p.Leu10PhefsTer6. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

#	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: Jun 17, 2024

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