10-13278111-GTT-GTTTT

Variant names:

• chr10-13278111-G-GTT
• rs3839912
• NM_006214.4:c.*188_*189dupAA

Variant summary

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

The NM_006214.4(PHYH):​c.*188_*189dupAA variant causes a 3 prime UTR 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 0.00010 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00047 (0 hom.)
• Consequence: PHYH NM_006214.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

PHYH (HGNC:8940): (phytanoyl-CoA 2-hydroxylase) This gene is a member of the PhyH family and encodes a peroxisomal protein that is involved in the alpha-oxidation of 3-methyl branched fatty acids. Specifically, this protein converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Mutations in this gene have been associated with Refsum disease (RD) and deficient protein activity has been associated with Zellweger syndrome and rhizomelic chondrodysplasia punctata. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHYH	NM_006214.4	c.*188_*189dupAA		3_prime_UTR_variant	Exon 9 of 9	ENST00000263038.9	NP_006205.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHYH	ENST00000263038	c.*188_*189dupAA		3_prime_UTR_variant	Exon 9 of 9	1	NM_006214.4	ENSP00000263038.4
PHYH	ENST00000396920	c.*188_*189dupAA		3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000380126.3
PHYH	ENST00000396913	c.*188_*189dupAA		3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000380121.2

Frequencies

GnomAD3 genomes AF: 0.0000995 AC: 15 AN: 150744 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: 0.000391

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00106

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000295

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000470 AC: 179 AN: 380932 Hom.: 0 Cov.: 0 AF XY: 0.000413 AC XY: 84 AN XY: 203594

Gnomad4 AFR exome AF: 0.000198

Gnomad4 AMR exome AF: 0.000173

Gnomad4 ASJ exome AF: 0.000407

Gnomad4 EAS exome AF: 0.000158

Gnomad4 SAS exome AF: 0.0000967

Gnomad4 FIN exome AF: 0.00238

Gnomad4 NFE exome AF: 0.000394

Gnomad4 OTH exome AF: 0.000514

GnomAD4 genome AF: 0.0000995 AC: 15 AN: 150744 Hom.: 0 Cov.: 0 AF XY: 0.000136 AC XY: 10 AN XY: 73486

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000391

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00106

Gnomad4 NFE AF: 0.0000295

Gnomad4 OTH AF: 0.00

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: rs3839912; hg19: chr10-13320111;