GeneBe

rs1051948

Variant names:

Variant summary

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

The NM_003322.6(TULP1):​c.*250C>T variant causes a 3 prime UTR 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: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TULP1
NM_003322.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0560

Publications

3 publications found
Variant links:
Genes affected
TULP1 (HGNC:12423): (TUB like protein 1) This gene encodes a member of the tubby-like gene family (TULPs). Members of this family have been identified in plants, vertebrates, and invertebrates. TULP proteins share a conserved C-terminal region of approximately 200 amino acid residues. The protein encoded by this gene is thought to play a role in the physiology of photoreceptors. Mutations in this gene are associated with recessive juvenile retinitis pigmentosa and Leber congenital amaurosis-15. [provided by RefSeq, Nov 2016]
TULP1 Gene-Disease associations (from GenCC):
  • retinitis pigmentosa 14
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
  • Leber congenital amaurosis 15
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • Leber congenital amaurosis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

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=-0.59).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003322.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TULP1
NM_003322.6
MANE Select
c.*250C>T
3_prime_UTR
Exon 15 of 15NP_003313.3
TULP1
NM_001289395.2
c.*250C>T
3_prime_UTR
Exon 14 of 14NP_001276324.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TULP1
ENST00000229771.11
TSL:1 MANE Select
c.*250C>T
3_prime_UTR
Exon 15 of 15ENSP00000229771.6
TULP1
ENST00000322263.8
TSL:1
c.*250C>T
3_prime_UTR
Exon 14 of 14ENSP00000319414.4
ENSG00000228559
ENST00000722038.1
n.456G>A
non_coding_transcript_exon
Exon 1 of 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
470538
Hom.:
0
Cov.:
5
AF XY:
0.00
AC XY:
0
AN XY:
246306
African (AFR)
AF:
0.00
AC:
0
AN:
12768
American (AMR)
AF:
0.00
AC:
0
AN:
18516
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13646
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30794
South Asian (SAS)
AF:
0.00
AC:
0
AN:
45388
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
29170
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1980
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
291720
Other (OTH)
AF:
0.00
AC:
0
AN:
26556
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
CADD
Benign
14
DANN
Benign
0.92
PhyloP100
-0.056

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: rs1051948; hg19: chr6-35465854; API