Genetic Variant AUTS2:p.Met1? (chr7-69599655-T-C) – ACMG Classification: Pathogenic (14 pts)

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PVS1PS1_ModeratePM2PP5_Moderate

The NM_015570.4(AUTS2):c.2T>C(p.Met1?) variant causes a start lost change involving the alteration of a non-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 (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AUTS2
NM_015570.4 start_lost

Scores

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 3.25

Publications

0 publications found

Variant links:

Genes affected

AUTS2 (HGNC:14262): (activator of transcription and developmental regulator AUTS2) This gene has been implicated in neurodevelopment and as a candidate gene for numerous neurological disorders, including autism spectrum disorders, intellectual disability, and developmental delay. Mutations in this gene have also been associated with non-neurological disorders, such as acute lymphoblastic leukemia, aging of the skin, early-onset androgenetic alopecia, and certain cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2014]

AUTS2 Gene-Disease associations (from GenCC):

autism spectrum disorder due to AUTS2 deficiency
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
syndromic intellectual disability
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen

AUTS2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 14 ACMG points.

PVS1

Start lost variant, next in-frame start position is after 9 pathogenic variants. Next in-frame start position is after 93 codons. Genomic position: 69599930. Lost 0.073 part of the original CDS.

PS1

Another start lost variant in NM_015570.4 (AUTS2) was described as [Pathogenic] in ClinVar

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 7-69599655-T-C is Pathogenic according to our data. Variant chr7-69599655-T-C is described in ClinVar as Pathogenic. ClinVar VariationId is 1033782.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015570.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
AUTS2	NM_015570.4	MANE Select	c.2T>C	p.Met1?	start_lost	Exon 1 of 19	NP_056385.1
AUTS2	NM_001127231.3		c.2T>C	p.Met1?	start_lost	Exon 1 of 18	NP_001120703.1
AUTS2	NM_001127232.3		c.2T>C	p.Met1?	start_lost	Exon 1 of 5	NP_001120704.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
AUTS2	ENST00000342771.10	TSL:1 MANE Select	c.2T>C	p.Met1?	start_lost	Exon 1 of 19	ENSP00000344087.4
AUTS2	ENST00000406775.6	TSL:1	c.2T>C	p.Met1?	start_lost	Exon 1 of 18	ENSP00000385263.2
AUTS2	ENST00000403018.3	TSL:1	c.2T>C	p.Met1?	start_lost	Exon 1 of 5	ENSP00000385572.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1148492

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

552394

African (AFR)

AF:

0.00

AC:

AN:

23130

American (AMR)

AF:

0.00

AC:

AN:

8970

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15166

East Asian (EAS)

AF:

0.00

AC:

AN:

26904

South Asian (SAS)

AF:

0.00

AC:

AN:

31700

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32606

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3106

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

960530

Other (OTH)

AF:

0.00

AC:

AN:

46380

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions as Germline

Significance:Pathogenic

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

Autism spectrum disorder due to AUTS2 deficiency (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.63

BayesDel_noAF

Benign

-0.18

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.034

Eigen

Benign

-0.16

Eigen_PC

Benign

-0.053

FATHMM_MKL

Benign

0.47

LIST_S2

Uncertain

0.90

M_CAP

Pathogenic

0.95

MetaRNN

Pathogenic

0.90

MetaSVM

Benign

-1.1

PhyloP100

3.2

PROVEAN

Benign

-0.44

REVEL

Benign

0.13

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

0.0030

Vest4

0.72

MutPred

0.77

Gain of phosphorylation at M1 (P = 0.002)

MVP

0.52

ClinPred

0.99

GERP RS

3.6

PromoterAI

-0.0014

Neutral

(source)

Varity_R

0.80

gMVP

0.18

Mutation Taster

=20/180

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over