chr1-151365622-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate

The NM_003944.4(SELENBP1):​c.985C>T​(p.His329Tyr) 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 Likely pathogenic (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SELENBP1
NM_003944.4 missense

Scores

8
7
4

Clinical Significance

Likely pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 9.19
Variant links:
Genes affected
SELENBP1 (HGNC:10719): (selenium binding protein 1) This gene encodes a member of the selenium-binding protein family. Selenium is an essential nutrient that exhibits potent anticarcinogenic properties, and deficiency of selenium may cause certain neurologic diseases. The effects of selenium in preventing cancer and neurologic diseases may be mediated by selenium-binding proteins, and decreased expression of this gene may be associated with several types of cancer. The encoded protein may play a selenium-dependent role in ubiquitination/deubiquitination-mediated protein degradation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Apr 2012]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.934
PP5
Variant 1-151365622-G-A is Pathogenic according to our data. Variant chr1-151365622-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 549497.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-151365622-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SELENBP1NM_003944.4 linkuse as main transcriptc.985C>T p.His329Tyr missense_variant 9/12 ENST00000368868.10
SELENBP1NM_001258289.2 linkuse as main transcriptc.1111C>T p.His371Tyr missense_variant 9/12
SELENBP1NM_001258288.2 linkuse as main transcriptc.799C>T p.His267Tyr missense_variant 8/11
SELENBP1XM_047433576.1 linkuse as main transcriptc.932C>T p.Ala311Val missense_variant 8/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SELENBP1ENST00000368868.10 linkuse as main transcriptc.985C>T p.His329Tyr missense_variant 9/121 NM_003944.4 P1Q13228-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Extra oral halitosis Pathogenic:1
Likely pathogenic, criteria provided, single submittercurationSIB Swiss Institute of BioinformaticsApr 16, 2018This variant is interpreted as a Likely Pathogenic, for Extraoral halitosis, Autosomal Recessive inheritance. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS3 => Well-established functional studies show a deleterious effect (PMID:29255262). -
Extraoral halitosis due to methanethiol oxidase deficiency Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMApr 19, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.70
BayesDel_addAF
Pathogenic
0.25
D
BayesDel_noAF
Uncertain
0.13
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.40
T;.;.
Eigen
Pathogenic
0.79
Eigen_PC
Pathogenic
0.75
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
0.98
D;D;D
M_CAP
Benign
0.034
D
MetaRNN
Pathogenic
0.93
D;D;D
MetaSVM
Benign
-0.56
T
MutationAssessor
Uncertain
2.8
M;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.59
T
PROVEAN
Pathogenic
-5.6
D;D;.
REVEL
Uncertain
0.47
Sift
Uncertain
0.0020
D;D;.
Sift4G
Uncertain
0.046
D;D;D
Polyphen
0.94
P;.;.
Vest4
0.92
MutPred
0.81
Loss of disorder (P = 0.1183);.;.;
MVP
0.40
MPC
0.23
ClinPred
0.99
D
GERP RS
5.2
Varity_R
0.81
gMVP
0.70

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1553204840; hg19: chr1-151338098; API