X-8732036-T-C

Variant names:

• chrX-8732036-T-C
• rs606231409
• NM_000216.4:c.1A>G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000216.4(ANOS1):​c.1A>G​(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000116 in 862,259 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.0000012 (0 hom. 0 hem.)
• Consequence: ANOS1 NM_000216.4 start_lost
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 3.47

Genes affected

ANOS1 (HGNC:6211): (anosmin 1) Mutations in this gene cause the X-linked Kallmann syndrome. The encoded protein is similar in sequence to proteins known to function in neural cell adhesion and axonal migration. In addition, this cell surface protein is N-glycosylated and may have anti-protease activity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Start lost variant, next in-frame start position is after 8 pathogenic variants. Next in-frame start position is after 335 codons. Genomic position: 8570558. Lost 0.491 part of the original CDS.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-8732036-T-C is Pathogenic according to our data. Variant chrX-8732036-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 140614.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANOS1	NM_000216.4	c.1A>G	p.Met1?	start_lost	Exon 1 of 14	ENST00000262648.8	NP_000207.2
ANOS1	XM_005274501.5	c.1A>G	p.Met1?	start_lost	Exon 1 of 9		XP_005274558.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANOS1	ENST00000262648.8	c.1A>G	p.Met1?	start_lost	Exon 1 of 14	1	NM_000216.4	ENSP00000262648.3

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 0.00000116 AC: 1 AN: 862259 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 262115

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000138

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 24

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Hypogonadotropic hypogonadism 1 with or without anosmia Pathogenic:1

May 01, 2013

Endocrinology Clinic, Seth G.S. Medical College

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

ANOS1-related disorder Pathogenic:1

Sep 29, 2023

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The ANOS1 c.1A>G variant is predicted to disrupt the translation initiation site (p.Met1?). This variant was previously reported in the hemizygous state in individuals with congenital hypogonadotropic hypogonadism/Kallmann syndrome (see, for example, Nair et al. 2016. PubMed ID: 26708526, figure 1, family 2; Amato et al. 2019. PubMed ID: 31200363). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.39
CADD	Benign	19
DANN	Benign	0.78
DEOGEN2	Benign	0.12	T
FATHMM_MKL	Uncertain	0.81	D
LIST_S2	Uncertain	0.90	D
M_CAP	Pathogenic	0.97	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Uncertain	-0.13	T
PROVEAN	Benign	-0.79	N
REVEL	Uncertain	0.52
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		0.71	P
Vest4		0.89
MutPred		1.0		Gain of catalytic residue at M1 (P = 0.1474);
MVP		0.99
ClinPred		0.54	D
GERP RS		3.0
Varity_R		0.92
gMVP		0.70

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: rs606231409; hg19: chrX-8700077;