5-53109712-CTG-TTT

Variant names:

• chr5-53109712-CTG-TTT
• NM_176806.4:c.16_18delCAGinsAAA
• MOCS2 p.Gln6Lys

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_176806.4(MOCS2):​c.16_18delCAGinsAAA​(p.Gln6Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q6R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MOCS2 NM_176806.4 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.20
• Publications: 0 publications found

Genes affected

MOCS2 (HGNC:7193): (molybdenum cofactor synthesis 2) Eukaryotic molybdoenzymes use a unique molybdenum cofactor (MoCo) consisting of a pterin, termed molybdopterin, and the catalytically active metal molybdenum. MoCo is synthesized from precursor Z by the heterodimeric enzyme molybdopterin synthase. The large and small subunits of molybdopterin synthase are both encoded from this gene by overlapping open reading frames. The proteins were initially thought to be encoded from a bicistronic transcript. They are now thought to be encoded from monocistronic transcripts. Alternatively spliced transcripts have been found for this locus that encode the large and small subunits. [provided by RefSeq, Jul 2008]

MOCS2-DT (HGNC:27417): (MOCS2 divergent transcript)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_176806.4. 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
	MOCS2	NM_176806.4	MANE Plus Clinical	c.16_18delCAGinsAAA	p.Gln6Lys	missense splice_region	N/A	NP_789776.1	O96033
	MOCS2	NM_004531.5	MANE Select	c.-633_-631delCAGinsAAA		5_prime_UTR	Exon 1 of 7	NP_004522.1	O96007
	MOCS2-DT	NR_034107.2		n.-130_-128delCTGinsTTT		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOCS2	ENST00000450852.8	TSL:1 MANE Plus Clinical	c.16_18delCAGinsAAA	p.Gln6Lys	missense splice_region	N/A	ENSP00000411022.3	O96033
	MOCS2	ENST00000396954.8	TSL:1 MANE Select	c.-633_-631delCAGinsAAA		5_prime_UTR	Exon 1 of 7	ENSP00000380157.3	O96007
	MOCS2	ENST00000855414.1		c.-50_-48delCAGinsAAA		splice_region	Exon 1 of 6	ENSP00000525473.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr5-52405542;