rs386833456

Variant names:

• chr7-107793855-ATTCTCTTGGCCTT-A
• rs386833456
• NM_000111.3:c.145_157delAAGGCCAAGAGAA

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_000111.3(SLC26A3):​c.145_157delAAGGCCAAGAGAA​(p.Lys49LeufsTer8) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC26A3 NM_000111.3 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 7.45

Genes affected

SLC26A3 (HGNC:3018): (solute carrier family 26 member 3) The protein encoded by this gene is a transmembrane glycoprotein that transports chloride ions across the cell membrane in exchange for bicarbonate ions. It is localized to the mucosa of the lower intestinal tract, particularly to the apical membrane of columnar epithelium and some goblet cells. The protein is essential for intestinal chloride absorption, and mutations in this gene have been associated with congenital chloride diarrhea. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 7-107793855-ATTCTCTTGGCCTT-A is Pathogenic according to our data. Variant chr7-107793855-ATTCTCTTGGCCTT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 55974.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr7-107793855-ATTCTCTTGGCCTT-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC26A3	NM_000111.3	c.145_157delAAGGCCAAGAGAA	p.Lys49LeufsTer8	frameshift_variant	Exon 3 of 21	ENST00000340010.10	NP_000102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A3	ENST00000340010.10	c.145_157delAAGGCCAAGAGAA	p.Lys49LeufsTer8	frameshift_variant	Exon 3 of 21	1	NM_000111.3	ENSP00000345873.5
SLC26A3	ENST00000453332.1	c.145_157delAAGGCCAAGAGAA	p.Lys49LeufsTer8	frameshift_variant	Exon 3 of 4	4		ENSP00000395955.1
SLC26A3	ENST00000379083.7	n.132-37_132-25delAAGGCCAAGAGAA		intron_variant	Intron 2 of 19	2		ENSP00000368375.3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

Submissions by phenotype

Congenital secretory diarrhea, chloride type Pathogenic:2

Dec 01, 2002

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386833456; hg19: chr7-107434300;