chrX-67723746-G-C

Position:

• chrX-67723746-G-C

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PS1 PM1 PM2 PM5 PP3_Moderate PP5_Moderate

The ENST00000374690.9(AR):​c.2668G>C​(p.Val890Leu) 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V890M) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 21)
• Consequence: AR ENST00000374690.9 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.76

Genes affected

AR (HGNC:644): (androgen receptor) The androgen receptor gene is more than 90 kb long and codes for a protein that has 3 major functional domains: the N-terminal domain, DNA-binding domain, and androgen-binding domain. The protein functions as a steroid-hormone activated transcription factor. Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. This gene contains 2 polymorphic trinucleotide repeat segments that encode polyglutamine and polyglycine tracts in the N-terminal transactivation domain of its protein. Expansion of the polyglutamine tract from the normal 9-34 repeats to the pathogenic 38-62 repeats causes spinal bulbar muscular atrophy (SBMA, also known as Kennedy's disease). Mutations in this gene are also associated with complete androgen insensitivity (CAIS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PS1: Transcript ENST00000374690.9 (AR) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 1338633
• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 5 uncertain in ENST00000374690.9
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-67723746-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 279690.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.848
• PP5: Variant X-67723746-G-C is Pathogenic according to our data. Variant chrX-67723746-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 430163.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-67723746-G-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AR	NM_000044.6	c.2668G>C	p.Val890Leu	missense_variant	8/8	ENST00000374690.9	NP_000035.2
AR	NM_001011645.3	c.1072G>C	p.Val358Leu	missense_variant	9/9		NP_001011645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AR	ENST00000374690.9	c.2668G>C	p.Val890Leu	missense_variant	8/8	1	NM_000044.6	ENSP00000363822	P1
AR	ENST00000396044.8	c.*29G>C		3_prime_UTR_variant	5/5	1		ENSP00000379359
AR	ENST00000396043.4	c.*1016G>C		3_prime_UTR_variant, NMD_transcript_variant	9/9	1		ENSP00000379358
AR	ENST00000612452.5	c.2668G>C	p.Val890Leu	missense_variant, NMD_transcript_variant	8/9	5		ENSP00000484033

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 21

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Feb 02, 2016

The V890L variant has been reported in an individual with ambiguous genitalia (Audi et al., 2010). The V890L variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The substitution occurs at a position that is conserved across species. The V890L variant occurs within the ligand binding domain, and a different missense variant at the same codon (V890M) has been published in association with complete and partial androgen insensitivity syndrome (Pinsky et al., 1992; DeBellis et al., 2004). Additionally, AR has a low rate of benign missense variation and missense variants are a common mechanism of disease in this gene. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.69	D
BayesDel_noAF	Pathogenic	0.76
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.10	T;.;.
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	D;D;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.85	D;D;D
MetaSVM	Pathogenic	0.98	D
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.76	T
PROVEAN	Benign	-2.2	.;N;D
REVEL	Pathogenic	0.95
Sift	Uncertain	0.0020	.;D;D
Sift4G	Uncertain	0.0040	D;D;D
Vest4		0.80
MVP		1.0
MPC		1.2
ClinPred		0.99	D
GERP RS		5.2
Varity_R		0.94
gMVP		0.96

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

LitVar

Other links and lift over

dbSNP: rs886041133; hg19: chrX-66943588;