GeneBe

12-56450041-CAAAA-CAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000648304.1(ENSG00000285528):​n.*1652_*1654dupTTT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

ENSG00000285528
ENST00000648304.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.669

Publications

1 publications found
Variant links:
Genes affected
MIP (HGNC:7103): (major intrinsic protein of lens fiber) Major intrinsic protein is a member of the water-transporting aquaporins as well as the original member of the MIP family of channel proteins. The function of the fiber cell membrane protein encoded by this gene is undetermined, yet this protein is speculated to play a role in intracellular communication. The MIP protein is expressed in the ocular lens and is required for correct lens function. This gene has been mapped among aquaporins AQP2, AQP5, and AQP6, in a potential gene cluster at 12q13. [provided by RefSeq, Jul 2008]
MIP Gene-Disease associations (from GenCC):
  • cataract 15 multiple types
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
  • cerulean cataract
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • early-onset lamellar cataract
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • early-onset nuclear cataract
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • early-onset posterior polar cataract
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • early-onset sutural cataract
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • total early-onset cataract
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIPNM_012064.4 linkc.*1236_*1238dupTTT 3_prime_UTR_variant Exon 4 of 4 ENST00000652304.1 NP_036196.1 P30301
MIPXM_011538354.2 linkc.*1236_*1238dupTTT 3_prime_UTR_variant Exon 6 of 6 XP_011536656.1
MIPXM_017019306.2 linkc.*1236_*1238dupTTT 3_prime_UTR_variant Exon 4 of 4 XP_016874795.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000285528ENST00000648304.1 linkn.*1652_*1654dupTTT non_coding_transcript_exon_variant Exon 4 of 4 ENSP00000497190.1 A0A3B3IS89
MIPENST00000652304.1 linkc.*1236_*1238dupTTT 3_prime_UTR_variant Exon 4 of 4 NM_012064.4 ENSP00000498622.1 P30301
ENSG00000285528ENST00000648304.1 linkn.*1652_*1654dupTTT 3_prime_UTR_variant Exon 4 of 4 ENSP00000497190.1 A0A3B3IS89

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
146524
Hom.:
0
Cov.:
0
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
146524
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
71038
African (AFR)
AF:
0.00
AC:
0
AN:
39900
American (AMR)
AF:
0.00
AC:
0
AN:
14704
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3446
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5088
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4664
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8870
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
308
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
66622
Other (OTH)
AF:
0.00
AC:
0
AN:
2014
Alfa
AF:
0.00
Hom.:
2029

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.67

Splicing

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

Publications

Other links and lift over

dbSNP: rs111463603; hg19: chr12-56843825; API