ENST00000373188.6:c.1150G>T

Variant names:

• chr6-39909055-C-A
• rs751603831
• ENST00000373188.6:c.1150G>T

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM2 PM5 PP3 PP5_Moderate

The ENST00000373188.6(MOCS1):​c.1150G>T​(p.Gly384Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G384S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 29)
• Consequence: MOCS1 ENST00000373188.6 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.84
• Publications: 0 publications found

Genes affected

MOCS1 (HGNC:7190): (molybdenum cofactor synthesis 1) Molybdenum cofactor biosynthesis is a conserved pathway leading to the biological activation of molybdenum. The protein encoded by this gene is involved in this pathway. This gene was originally thought to produce a bicistronic mRNA with the potential to produce two proteins (MOCS1A and MOCS1B) from adjacent open reading frames. However, only the first open reading frame (MOCS1A) has been found to encode a protein from the putative bicistronic mRNA, whereas additional splice variants are likely to produce a fusion between the two open reading frames. This gene is defective in patients with molybdenum cofactor deficiency, type A. A related pseudogene has been identified on chromosome 16. [provided by RefSeq, Nov 2017]

MOCS1 Gene-Disease associations (from GenCC):

• sulfite oxidase deficiency due to molybdenum cofactor deficiency type A

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr6-39909054-C-A is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 1388733.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 6-39909055-C-A is Pathogenic according to our data. Variant chr6-39909055-C-A is described in ClinVar as Pathogenic. ClinVar VariationId is 2005863.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000373188.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOCS1	NM_001358530.2	MANE Select	c.1150G>T	p.Glu384*	stop_gained splice_region	Exon 10 of 11	NP_001345459.1	Q9NZB8-1
	MOCS1	NM_001075098.4		c.1150G>T	p.Gly384Cys	missense	Exon 10 of 11	NP_001068566.1	Q9NZB8-5
	MOCS1	NM_005943.6		c.1150G>T	p.Gly384Cys	missense	Exon 9 of 10	NP_005934.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOCS1	ENST00000373188.6	TSL:1	c.1150G>T	p.Gly384Cys	missense	Exon 10 of 11	ENSP00000362284.2	Q9NZB8-5
	MOCS1	ENST00000340692.10	TSL:5 MANE Select	c.1150G>T	p.Glu384*	stop_gained splice_region	Exon 10 of 11	ENSP00000344794.5	Q9NZB8-1
	MOCS1	ENST00000373181.8	TSL:1	n.841+780G>T		intron	N/A	ENSP00000362277.4	Q9NZB8-4

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 29

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Sulfite oxidase deficiency due to molybdenum cofactor deficiency type A (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Uncertain	-0.040
CADD	Pathogenic	52
DANN	Uncertain	1.0
Eigen	Pathogenic	0.85
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		7.8
Vest4		0.61
ClinPred		1.0	D
GERP RS		5.2
Mutation Taster		=30/170	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.63		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.63		Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs751603831; hg19: chr6-39876831;