chr1-154928774-AAAATAAATAAATAAATAAAT-A

Variant names:

• chr1-154928774-AAAATAAATAAATAAATAAAT-A
• rs55948301
• NM_006556.4:c.312+230_312+249delATTTATTTATTTATTTATTT

Variant summary

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

The NM_006556.4(PMVK):​c.312+230_312+249delATTTATTTATTTATTTATTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000014 (0 hom., cov: 0)
• Consequence: PMVK NM_006556.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.907

Genes affected

PMVK (HGNC:9141): (phosphomevalonate kinase) This gene encodes a peroxisomal enzyme that is a member of the galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase (GHMP) family of ATP-dependent enzymes. The encoded protein catalyzes the conversion of mevalonate 5-phosphate to mevalonate 5-diphosphate, which is the fifth step in the mevalonate pathway of isoprenoid biosynthesis. Mutations in this gene are linked to certain types of porokeratosis including disseminated superficial porokeratosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PMVK	NM_006556.4	c.312+230_312+249delATTTATTTATTTATTTATTT		intron_variant	Intron 3 of 4	ENST00000368467.4	NP_006547.1
PMVK	NM_001323011.3	c.270+230_270+249delATTTATTTATTTATTTATTT		intron_variant	Intron 3 of 4		NP_001309940.1
PMVK	NM_001323012.3	c.87+230_87+249delATTTATTTATTTATTTATTT		intron_variant	Intron 3 of 4		NP_001309941.1
PMVK	NM_001348696.2	c.87+230_87+249delATTTATTTATTTATTTATTT		intron_variant	Intron 3 of 4		NP_001335625.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PMVK	ENST00000368467.4	c.312+230_312+249delATTTATTTATTTATTTATTT		intron_variant	Intron 3 of 4	1	NM_006556.4	ENSP00000357452.3

Frequencies

GnomAD3 genomes AF: 0.0000141 AC: 2 AN: 142024 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000221

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000152

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000141 AC: 2 AN: 142024 Hom.: 0 Cov.: 0 AF XY: 0.0000291 AC XY: 2 AN XY: 68614

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000221

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000152

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55948301; hg19: chr1-154901250;