rs387907184

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5

The ENST00000521508.2(ALG11):​c.953A>C​(p.Gln318Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

ALG11
ENST00000521508.2 missense

Scores

11
6
2

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 8.89
Variant links:
Genes affected
ALG11 (HGNC:32456): (ALG11 alpha-1,2-mannosyltransferase) This gene encodes a GDP-Man:Man3GlcNAc2-PP-dolichol-alpha1,2-mannosyltransferase which is localized to the cytosolic side of the endoplasmic reticulum (ER) and catalyzes the transfer of the fourth and fifth mannose residue from GDP-mannose (GDP-Man) to Man3GlcNAc2-PP-dolichol and Man4GlcNAc2-PP-dolichol resulting in the production of Man5GlcNAc2-PP-dolichol. Mutations in this gene are associated with congenital disorder of glycosylation type Ip (CDGIP). This gene overlaps but is distinct from the UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast) gene. A pseudogene of the GDP-Man:Man3GlcNAc2-PP-dolichol-alpha1,2-mannosyltransferase has been identified on chromosome 19. [provided by RefSeq, Aug 2010]
UTP14C (HGNC:20321): (UTP14C small subunit processome component) Predicted to be involved in several processes, including meiotic cell cycle; rRNA processing; and spermatogenesis. Located in cytosol and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.935
PP5
Variant 13-52024683-A-C is Pathogenic according to our data. Variant chr13-52024683-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 31647.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr13-52024683-A-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ALG11NM_001004127.3 linkuse as main transcriptc.953A>C p.Gln318Pro missense_variant 3/4 ENST00000521508.2 NP_001004127.2
ALG11NR_036571.3 linkuse as main transcriptn.66-3636A>C intron_variant, non_coding_transcript_variant
UTP14CNM_021645.6 linkuse as main transcript upstream_gene_variant ENST00000521776.2 NP_067677.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ALG11ENST00000521508.2 linkuse as main transcriptc.953A>C p.Gln318Pro missense_variant 3/41 NM_001004127.3 ENSP00000430236 P4
UTP14CENST00000521776.2 linkuse as main transcript upstream_gene_variant 1 NM_021645.6 ENSP00000428619 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

ALG11-congenital disorder of glycosylation Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMMar 01, 2012- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.85
BayesDel_addAF
Pathogenic
0.43
D
BayesDel_noAF
Pathogenic
0.38
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.87
D
Eigen
Pathogenic
1.0
Eigen_PC
Pathogenic
0.98
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.95
D
M_CAP
Uncertain
0.16
D
MetaRNN
Pathogenic
0.93
D
MetaSVM
Uncertain
0.68
D
MutationAssessor
Pathogenic
3.7
H
MutationTaster
Benign
1.0
D;D
PrimateAI
Benign
0.48
T
PROVEAN
Pathogenic
-5.3
D
REVEL
Pathogenic
0.85
Sift
Uncertain
0.0050
D
Sift4G
Uncertain
0.0090
D
Polyphen
1.0
D
Vest4
0.89
MutPred
0.70
Gain of catalytic residue at L317 (P = 2e-04);
MVP
0.92
MPC
0.34
ClinPred
1.0
D
GERP RS
6.2
Varity_R
0.98
gMVP
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs387907184; hg19: chr13-52598819; API