2-44275554-A-G

Position:

• chr2-44275554-A-G

Variant summary

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

The NM_000341.4(SLC3A1):​c.19A>G​(p.Lys7Glu) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: SLC3A1 NM_000341.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.50

Genes affected

SLC3A1 (HGNC:11025): (solute carrier family 3 member 1) This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

ENSG00000285542 (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=0.245128).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC3A1	NM_000341.4	c.19A>G	p.Lys7Glu	missense_variant	1/10	ENST00000260649.11	NP_000332.2
SLC3A1	XM_011533047.4	c.19A>G	p.Lys7Glu	missense_variant	1/10		XP_011531349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC3A1	ENST00000260649.11	c.19A>G	p.Lys7Glu	missense_variant	1/10	1	NM_000341.4	ENSP00000260649.6
ENSG00000285542	ENST00000649044.1	n.*30A>G		non_coding_transcript_exon_variant	6/15			ENSP00000497083.1
ENSG00000285542	ENST00000649044.1	n.*30A>G		3_prime_UTR_variant	6/15			ENSP00000497083.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Cystinuria Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Feb 04, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Uncertain	0.092	D
BayesDel_noAF	Benign	-0.11
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.012	T;T;T;.;.;.
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.37
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.75	T;T;T;T;T;T
M_CAP	Uncertain	0.094	D
MetaRNN	Benign	0.25	T;T;T;T;T;T
MetaSVM	Pathogenic	0.80	D
MutationAssessor	Uncertain	2.2	.;M;.;M;M;M
PrimateAI	Benign	0.32	T
PROVEAN	Benign	-0.83	.;N;N;N;N;N
REVEL	Uncertain	0.40
Sift	Uncertain	0.0080	.;D;D;D;D;D
Sift4G	Benign	0.13	T;T;T;T;T;T
Polyphen		0.52, 0.67	.;P;P;.;.;.
Vest4		0.44
MutPred		0.19		Loss of ubiquitination at K7 (P = 6e-04);Loss of ubiquitination at K7 (P = 6e-04);Loss of ubiquitination at K7 (P = 6e-04);Loss of ubiquitination at K7 (P = 6e-04);Loss of ubiquitination at K7 (P = 6e-04);Loss of ubiquitination at K7 (P = 6e-04);
MVP		0.92
MPC		0.0059
ClinPred		0.38	T
GERP RS		1.1
Varity_R		0.15
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: chr2-44502693;