rs137853158

Variant names:

• chr15-48229278-G-T
• rs137853158
• NM_000338.3:c.814G>T

Variant summary

Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PM2 PP3_Strong PP5

The NM_000338.3(SLC12A1):​c.814G>T​(p.Val272Phe) 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V272A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC12A1 NM_000338.3 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.60
• Publications: 4 publications found

Genes affected

SLC12A1 (HGNC:10910): (solute carrier family 12 member 1) This gene encodes a kidney-specific sodium-potassium-chloride cotransporter that is expressed on the luminal membrane of renal epithelial cells of the thick ascending limb of Henle's loop and the macula densa. It plays a key role in concentrating urine and accounts for most of the NaCl resorption. It is sensitive to such diuretics as furosemide and bumetanide. Some Bartter-like syndromes result from defects in this gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their biological validity in humans has not been experimentally proven.[provided by RefSeq, May 2010]

SLC12A1 Gene-Disease associations (from GenCC):

• Bartter disease type 1

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• antenatal Bartter syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

LOC128966560 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.984
• PP5: Variant 15-48229278-G-T is Pathogenic according to our data. Variant chr15-48229278-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 8753.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC12A1	NM_000338.3	c.814G>T	p.Val272Phe	missense_variant	Exon 6 of 27	ENST00000380993.8	NP_000329.2
SLC12A1	NM_001184832.2	c.814G>T	p.Val272Phe	missense_variant	Exon 6 of 27		NP_001171761.1
SLC12A1	NM_001384136.1	c.814G>T	p.Val272Phe	missense_variant	Exon 6 of 27		NP_001371065.1
LOC128966560	XR_932204.4	n.222+678C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC12A1	ENST00000380993.8	c.814G>T	p.Val272Phe	missense_variant	Exon 6 of 27	5	NM_000338.3	ENSP00000370381.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Bartter disease type 1 Pathogenic:1

Jun 01, 1996

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.85	.;.;.;D;.;D;D;.;.
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	.;D;D;.;D;.;D;D;D
M_CAP	Pathogenic	0.62	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.7	H;.;.;H;.;H;H;H;.
PhyloP100		9.6
PrimateAI	Uncertain	0.71	T
PROVEAN	Pathogenic	-4.4	.;.;.;.;D;D;D;D;D
REVEL	Pathogenic	0.97
Sift	Uncertain	0.0030	.;.;.;.;D;D;D;D;D
Sift4G	Uncertain	0.054	.;.;T;.;D;D;D;D;D
Polyphen		1.0	.;.;.;D;.;D;D;.;D
Vest4		0.96, 0.94, 0.89
MutPred		0.92		Loss of catalytic residue at V272 (P = 0.2753);.;.;Loss of catalytic residue at V272 (P = 0.2753);.;Loss of catalytic residue at V272 (P = 0.2753);Loss of catalytic residue at V272 (P = 0.2753);Loss of catalytic residue at V272 (P = 0.2753);Loss of catalytic residue at V272 (P = 0.2753);
MVP		0.99
MPC		0.72
ClinPred		1.0	D
GERP RS		5.8
Varity_R		0.79
gMVP		0.95
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs137853158; hg19: chr15-48521475;