17-7583724-G-C

Variant names:

• chr17-7583724-G-C
• rs551554693
• NM_001330073.1:c.-139G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001330073.1(MPDU1):​c.-139G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MPDU1 NM_001330073.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921
• Publications: 0 publications found

Genes affected

MPDU1 (HGNC:7207): (mannose-P-dolichol utilization defect 1) This gene encodes an endoplasmic reticulum membrane protein that is required for utilization of the mannose donor mannose-P-dolichol in the synthesis of lipid-linked oligosaccharides and glycosylphosphatidylinositols. Mutations in this gene result in congenital disorder of glycosylation type If. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

MPDU1-AS1 (HGNC:40379): (MPDU1 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330073.1. 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
	MPDU1	NM_001330073.1		c.-139G>C		5_prime_UTR	Exon 1 of 6	NP_001317002.1	J3QW43
	MPDU1	NR_024603.1		n.78G>C		non_coding_transcript_exon	Exon 1 of 7
	MPDU1-AS1	NR_136401.2		n.175+194C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPDU1	ENST00000582151.1	TSL:6	c.-139G>C		5_prime_UTR	Exon 1 of 1	ENSP00000462500.1	J3KSI4
	MPDU1-AS1	ENST00000572046.3	TSL:3	n.19C>G		non_coding_transcript_exon	Exon 1 of 2
	MPDU1	ENST00000572936.5	TSL:5	n.-139G>C		non_coding_transcript_exon	Exon 1 of 7	ENSP00000459306.1	I3L1D2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 724450 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 388968

African (AFR) AF: 0.00 AC: 0 AN: 19650

American (AMR) AF: 0.00 AC: 0 AN: 43668

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21612

East Asian (EAS) AF: 0.00 AC: 0 AN: 36518

South Asian (SAS) AF: 0.00 AC: 0 AN: 71156

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40758

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2994

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 451564

Other (OTH) AF: 0.00 AC: 0 AN: 36530

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		0.92
PromoterAI		0.096	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs551554693; hg19: chr17-7487042;