rs1553203137

Variant names:

• chr1-100011380-C-A
• NM_012243.3:c.481C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-100011380-C-A
• chr1-100011380-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_012243.3(SLC35A3):​c.481C>A​(p.Gln161Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000727 in 1,374,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q161Q) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: SLC35A3 NM_012243.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

Genes affected

SLC35A3 (HGNC:11023): (solute carrier family 35 member A3) This gene encodes a UDP-N-acetylglucosamine transporter found in the golgi apparatus membrane. In cattle, a missense mutation in this gene causes complex vertebral malformation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ENSG00000283761 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.080141336).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A3	NM_012243.3	c.481C>A	p.Gln161Lys	missense_variant	Exon 5 of 8	ENST00000533028.8	NP_036375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A3	ENST00000533028.8	c.481C>A	p.Gln161Lys	missense_variant	Exon 5 of 8	1	NM_012243.3	ENSP00000433849.1
ENSG00000283761	ENST00000639037.1	c.481C>A	p.Gln161Lys	missense_variant	Exon 5 of 17	5		ENSP00000492745.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.27e-7 AC: 1 AN: 1374860 Hom.: 0 Cov.: 25 AF XY: 0.00000146 AC XY: 1 AN XY: 683646

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000177

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	20
DANN	Benign	0.56
DEOGEN2	Benign	0.063	.;T;T;.;.;.;.;T;.;.;.;.;.;.;.;.
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.018
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.85	T;.;.;T;T;T;T;T;T;T;T;T;T;D;D;D
M_CAP	Benign	0.0021	T
MetaRNN	Benign	0.080	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.41	.;N;N;.;N;.;.;N;.;.;.;.;.;.;.;.
PrimateAI	Benign	0.45	T
PROVEAN	Benign	-0.25	.;.;N;.;.;.;.;N;.;.;.;.;.;N;.;.
REVEL	Benign	0.088
Sift	Benign	1.0	.;.;T;.;.;.;.;T;.;.;.;.;.;T;.;.
Sift4G	Benign	0.88	.;T;T;.;.;.;.;T;.;.;.;.;.;T;.;.
Polyphen		0.0	.;B;B;.;.;.;.;B;.;.;.;.;.;.;.;.
Vest4		0.18, 0.19, 0.16
MutPred		0.36		Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);.;Gain of ubiquitination at Q161 (P = 0.0051);.;Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);.;Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);.;Gain of ubiquitination at Q161 (P = 0.0051);Gain of ubiquitination at Q161 (P = 0.0051);
MVP		0.67
ClinPred		0.18	T
GERP RS		5.5
Varity_R		0.30
gMVP		0.10

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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: chr1-100476936;