NM_031274.5:c.934T>C

Variant names:

• chrX-105219260-A-G
• NM_031274.5:c.934T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_031274.5(TEX13A):​c.934T>C​(p.Ser312Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: TEX13A NM_031274.5 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0630
• Publications: 0 publications found

Genes affected

TEX13A (HGNC:11735): (testis expressed 13A) This gene is similar to a mouse gene that is expressed in the testis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

IL1RAPL2 (HGNC:5997): (interleukin 1 receptor accessory protein like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. This protein is similar to the interleukin 1 accessory proteins, and is most closely related to interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). This gene and IL1RAPL1 are located at a region on chromosome X that is associated with X-linked non-syndromic cognitive disability. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.052756608).
• BP6: Variant X-105219260-A-G is Benign according to our data. Variant chrX-105219260-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3176272.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031274.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX13A	NM_031274.5	MANE Select	c.934T>C	p.Ser312Pro	missense	Exon 3 of 3	NP_112564.1	Q9BXU3
	IL1RAPL2	NM_017416.2	MANE Select	c.357-14558A>G		intron	N/A	NP_059112.1	Q9NP60
	TEX13A	NM_001291277.2		c.934T>C	p.Ser312Pro	missense	Exon 3 of 3	NP_001278206.1	Q9BXU3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX13A	ENST00000600991.6	TSL:1 MANE Select	c.934T>C	p.Ser312Pro	missense	Exon 3 of 3	ENSP00000471604.2	Q9BXU3
	TEX13A	ENST00000609007.3	TSL:1	c.934T>C	p.Ser312Pro	missense	Exon 3 of 3	ENSP00000477478.2	Q9BXU3
	IL1RAPL2	ENST00000372582.6	TSL:1 MANE Select	c.357-14558A>G		intron	N/A	ENSP00000361663.1	Q9NP60

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 22

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0034	T
FATHMM_MKL	Benign	0.00046	N
LIST_S2	Benign	0.29	T
M_CAP	Benign	0.0038	T
MetaRNN	Benign	0.053	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.36	N
PhyloP100		0.063
PrimateAI	Benign	0.34	T
Sift4G	Benign	0.49	T
Polyphen		0.0	B
Vest4		0.030
MutPred		0.14		Loss of glycosylation at S312 (P = 0.021)
MVP		0.040
ClinPred		0.18	T
GERP RS		1.3
Varity_R		0.090
gMVP		0.024
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

hg19: chrX-104463942;