rs33912867

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_181776.3(SLC36A2):c.*65_*76delTTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000792 in 896,212 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000080 ( 0 hom. )

Consequence

SLC36A2
NM_181776.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Publications

1 publications found

Variant links:

Genes affected

SLC36A2 (HGNC:18762): (solute carrier family 36 member 2) This gene encodes a pH-dependent proton-coupled amino acid transporter that belongs to the amino acid auxin permease 1 protein family. The encoded protein primarily transports small amino acids such as glycine, alanine and proline. Mutations in this gene are associated with iminoglycinuria and hyperglycinuria. [provided by RefSeq, Sep 2010]

SLC36A2 Gene-Disease associations (from GenCC):

iminoglycinuria
Inheritance: AR, AD Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, ClinGen, Orphanet
hyperglycinuria
Inheritance: SD, AD, AR Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

SLC36A2 links:

ENSG00000297368 (HGNC:):

ENSG00000297368 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181776.3. 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
	SLC36A2	NM_181776.3	MANE Select	c.65_76delTTTTTTTTTTTT		3_prime_UTR	Exon 10 of 10	NP_861441.2	Q495M3-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC36A2	ENST00000335244.9	TSL:1 MANE Select	c.65_76delTTTTTTTTTTTT	3_prime_UTR	Exon 10 of 10	ENSP00000334223.4	Q495M3-1
SLC36A2	ENST00000518280.5	TSL:1	n.988_999delTTTTTTTTTTTT	non_coding_transcript_exon	Exon 9 of 9	ENSP00000428453.1	E5RGH8
SLC36A2	ENST00000518617.5	TSL:1	n.1085_1096delTTTTTTTTTTTT	non_coding_transcript_exon	Exon 10 of 10	ENSP00000430149.1	E5RGH8

Frequencies

GnomAD3 genomes

AF:

0.0000591

AC:

AN:

50738

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000885

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000272

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000338

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000804

AC:

AN:

845472

Hom.:

AF XY:

0.0000746

AC XY:

AN XY:

428970

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18720

American (AMR)

AF:

0.00

AC:

AN:

21166

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15302

East Asian (EAS)

AF:

0.0000416

AC:

AN:

24020

South Asian (SAS)

AF:

0.00

AC:

AN:

54540

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26200

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2572

European-Non Finnish (NFE)

AF:

0.000104

AC:

AN:

647198

Other (OTH)

AF:

0.00

AC:

AN:

35754

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.606

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000591

AC:

AN:

50740

Hom.:

Cov.:

AF XY:

0.0000895

AC XY:

AN XY:

22344

show subpopulations

African (AFR)

AF:

0.0000883

AC:

AN:

11324

American (AMR)

AF:

0.000272

AC:

AN:

3670

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1712

East Asian (EAS)

AF:

0.00

AC:

AN:

1378

South Asian (SAS)

AF:

0.00

AC:

AN:

998

European-Finnish (FIN)

AF:

0.00

AC:

AN:

924

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000338

AC:

AN:

29592

Other (OTH)

AF:

0.00

AC:

AN:

664

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.592

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over