GeneBe

rs11081576

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006701.5(TXNL4A):​c.257+201G>T variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TXNL4A
NM_006701.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.492

Publications

7 publications found
Variant links:
Genes affected
TXNL4A (HGNC:30551): (thioredoxin like 4A) The protein encoded by this gene is a member of the U5 small ribonucleoprotein particle (snRNP), and is involved in pre-mRNA splicing. This protein contains a thioredoxin-like fold and it is expected to interact with multiple proteins. Protein-protein interactions have been observed with the polyglutamine tract-binding protein 1 (PQBP1). Mutations in both the coding region and promoter region of this gene have been associated with Burn-McKeown syndrome, which is a rare disorder characterized by craniofacial dysmorphisms, cardiac defects, hearing loss, and bilateral choanal atresia. A pseudogene of this gene is found on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]
TXNL4A Gene-Disease associations (from GenCC):
  • choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome
    Inheritance: AR, Unknown Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006701.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TXNL4A
NM_006701.5
MANE Select
c.257+201G>T
intron
N/ANP_006692.1P83876
TXNL4A
NM_001305557.2
c.233+201G>T
intron
N/ANP_001292486.1
TXNL4A
NM_001303471.3
c.140+201G>T
intron
N/ANP_001290400.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TXNL4A
ENST00000269601.10
TSL:1 MANE Select
c.257+201G>T
intron
N/AENSP00000269601.4P83876
TXNL4A
ENST00000585474.5
TSL:1
c.44+201G>T
intron
N/AENSP00000465572.1K7ESL1
TXNL4A
ENST00000355491.5
TSL:1
n.257+201G>T
intron
N/AENSP00000347678.4O14835

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
392552
Hom.:
0
Cov.:
3
AF XY:
0.00
AC XY:
0
AN XY:
205880
African (AFR)
AF:
0.00
AC:
0
AN:
9552
American (AMR)
AF:
0.00
AC:
0
AN:
11754
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
12544
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26974
South Asian (SAS)
AF:
0.00
AC:
0
AN:
31626
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
31900
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1800
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
243188
Other (OTH)
AF:
0.00
AC:
0
AN:
23214
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.50
DANN
Benign
0.61
PhyloP100
-0.49

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

Other links and lift over

dbSNP: rs11081576; hg19: chr18-77737397; API