chr6-148533885-G-A

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 1P and 1B. PP5BP4

The NM_015278.5(SASH1):c.1849G>A(p.Glu617Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000028 ( 0 hom. )

Consequence

SASH1
NM_015278.5 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic no assertion criteria provided P:2

Conservation

PhyloP100: 10.0

Publications

10 publications found

Variant links:

Genes affected

SASH1 (HGNC:19182): (SAM and SH3 domain containing 1) This gene encodes a scaffold protein involved in the TLR4 signaling pathway that may stimulate cytokine production and endothelial cell migration in response to invading pathogens. The encoded protein has also been described as a potential tumor suppressor that may negatively regulate proliferation, apoptosis, and invasion of cancer cells, and reduced expression of this gene has been observed in multiple human cancers. Mutations in this gene may be associated with abnormal skin pigmentation in human patients. [provided by RefSeq, Oct 2016]

SASH1 Gene-Disease associations (from GenCC):

dyschromatosis universalis hereditaria 1
Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics
familial generalized lentiginosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
pigmentation defects-palmoplantar keratoderma-skin carcinoma syndrome
Inheritance: AR Classification: SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)

SASH1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

PP5

Variant 6-148533885-G-A is Pathogenic according to our data. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-148533885-G-A is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 156162.Status of the report is no_assertion_criteria_provided, 0 stars.

BP4

Computational evidence support a benign effect (MetaRNN=0.3146152). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SASH1	NM_015278.5 link	c.1849G>A	p.Glu617Lys	missense_variant	Exon 15 of 20	ENST00000367467.8	NP_056093.3	O94885

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SASH1	ENST00000367467.8 link	c.1849G>A	p.Glu617Lys	missense_variant	Exon 15 of 20	1	NM_015278.5	ENSP00000356437.3		O94885

Frequencies

GnomAD3 genomes

AF:

0.0000789

AC:

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000588

Gnomad OTH

AF:

0.000478

GnomAD2 exomes

AF:

0.0000676

AC:

AN:

251404

AF XY:

0.0000515

show subpopulations

Gnomad AFR exome

AF:

0.0000616

Gnomad AMR exome

AF:

0.000318

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.0000352

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000280

AC:

AN:

1461800

Hom.:

Cov.:

AF XY:

0.0000275

AC XY:

AN XY:

727196

show subpopulations

African (AFR)

AF:

0.0000597

AC:

AN:

33476

American (AMR)

AF:

0.000268

AC:

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26134

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86254

European-Finnish (FIN)

AF:

0.0000374

AC:

AN:

53414

Middle Eastern (MID)

AF:

0.000520

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.0000180

AC:

AN:

1111952

Other (OTH)

AF:

0.0000331

AC:

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

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:

0.0000789

AC:

AN:

152158

Hom.:

Cov.:

AF XY:

0.000121

AC XY:

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.0000724

AC:

AN:

41450

American (AMR)

AF:

0.000131

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.000207

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0000942

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000588

AC:

AN:

68020

Other (OTH)

AF:

0.000478

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

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.:

Bravo

AF:

0.0000604

ExAC

AF:

0.0000741

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Cancer, alopecia, pigment dyscrasia, onychodystrophy, and keratoderma

Pathogenic:1

Jul 01, 2015

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Alopecia;C4551675:Palmoplantar keratoderma;C4552243:dyschromatosis;CN219573:Ungual dystrophy;CN219574:spino-cellular carcinoma

Pathogenic:1

Jun 21, 2014

Laboratoire de Biologie Moléculaire, Centre Hospitalo-Universitaire

Significance:Likely pathogenic

Review Status:no assertion criteria provided

Collection Method:case-control

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.32

CADD

Uncertain

(source)

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.17

T;T

Eigen

Uncertain

0.38

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.96

D;D

M_CAP

Benign

0.012

MetaRNN

Benign

0.31

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.2

M;.

PhyloP100

PrimateAI

Uncertain

0.64

PROVEAN

Uncertain

-2.7

D;.

REVEL

Benign

0.21

Sift

Uncertain

0.0070

D;.

Sift4G

Uncertain

0.013

D;D

Polyphen

0.80

P;.

Vest4

0.63

MutPred

0.24

Gain of MoRF binding (P = 0.0106);.;

MVP

0.57

MPC

0.17

ClinPred

0.19

GERP RS

5.1

Varity_R

0.50

gMVP

0.73

Mutation Taster

=66/34

disease causing (ClinVar)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over