NM_000276.4:c.12_13delGCinsTA

Variant names:

• chrX-129540451-GC-TA
• NM_000276.4:c.12_13delGCinsTA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000276.4(OCRL):​c.12_13delGCinsTA​(p.Leu5Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 21)
• Consequence: OCRL NM_000276.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.70

Genes affected

OCRL (HGNC:8108): (OCRL inositol polyphosphate-5-phosphatase) This gene encodes an inositol polyphosphate 5-phosphatase. This protein is involved in regulating membrane trafficking and is located in numerous subcellular locations including the trans-Golgi network, clathrin-coated vesicles and, endosomes and the plasma membrane. This protein may also play a role in primary cilium formation. Mutations in this gene cause oculocerebrorenal syndrome of Lowe and also Dent disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OCRL	NM_000276.4	c.12_13delGCinsTA	p.Leu5Ile	missense_variant		ENST00000371113.9	NP_000267.2
OCRL	NM_001318784.2	c.12_13delGCinsTA	p.Leu5Ile	missense_variant			NP_001305713.1
OCRL	NM_001587.4	c.12_13delGCinsTA	p.Leu5Ile	missense_variant			NP_001578.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OCRL	ENST00000371113.9	c.12_13delGCinsTA	p.Leu5Ile	missense_variant		1	NM_000276.4	ENSP00000360154.4
OCRL	ENST00000357121.5	c.12_13delGCinsTA	p.Leu5Ile	missense_variant		1		ENSP00000349635.5
OCRL	ENST00000691455.1	n.12_13delGCinsTA		non_coding_transcript_exon_variant	Exon 1 of 18			ENSP00000510265.1
OCRL	ENST00000486673.1	n.91+512_91+513delGCinsTA		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes Cov.: 21

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

GnomAD4 genome Cov.: 21

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Apr 26, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-128674428;