Variant 22-36999930-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001163857.2(CIMIP4):c.544C>T(p.Pro182Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,461,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 29)

Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

CIMIP4
NM_001163857.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0800

Variant links:

Genes affected

CIMIP4 (HGNC:28568): (ciliary microtubule inner protein 4)

CIMIP4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.046617478).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIMIP4	NM_001163857.2 link	c.544C>T	p.Pro182Ser	missense_variant	4/6	ENST00000381821.2	NP_001157329.1	O43247-1
CIMIP4	NM_178552.4 link	c.289C>T	p.Pro97Ser	missense_variant	4/6		NP_848647.1	O43247-2
CIMIP4	XM_011530165.3 link	c.544C>T	p.Pro182Ser	missense_variant	5/7		XP_011528467.1	O43247-1
CIMIP4	XM_011530166.2 link	c.289C>T	p.Pro97Ser	missense_variant	4/6		XP_011528468.1	O43247-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TEX33	ENST00000381821.2 link	c.544C>T	p.Pro182Ser	missense_variant	4/6	1	NM_001163857.2	ENSP00000371243.1	O43247-1
TEX33	ENST00000402860.7 link	c.289C>T	p.Pro97Ser	missense_variant	4/6	1		ENSP00000385179.3	O43247-2
TEX33	ENST00000405091.6 link	c.544C>T	p.Pro182Ser	missense_variant	5/7	5		ENSP00000386118.2	O43247-1
TEX33	ENST00000442538.5 link	c.118C>T	p.Pro40Ser	missense_variant	2/4	3		ENSP00000406640.1	H0Y6N4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000318

AC:

AN:

251342

Hom.:

AF XY:

0.0000589

AC XY:

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000261

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000164

AC:

AN:

1461728

Hom.:

Cov.:

AF XY:

0.0000303

AC XY:

AN XY:

727182

show subpopulations

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:

0.000278

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000412

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 02, 2024

The c.544C>T (p.P182S) alteration is located in exon 4 (coding exon 3) of the TEX33 gene. This alteration results from a C to T substitution at nucleotide position 544, causing the proline (P) at amino acid position 182 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.044

.;T;T

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.037

LIST_S2

Benign

0.61

T;.;T

M_CAP

Benign

0.0095

MetaRNN

Benign

0.047

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.3

.;L;L

PrimateAI

Benign

0.28

PROVEAN

Uncertain

-3.9

D;D;D

REVEL

Benign

0.053

Sift

Benign

0.19

T;T;T

Sift4G

Benign

0.23

T;T;T

Polyphen

0.23

.;B;B

Vest4

0.14

MutPred

0.19

.;Gain of phosphorylation at P182 (P = 0.0423);Gain of phosphorylation at P182 (P = 0.0423);

MVP

0.055

MPC

0.18

ClinPred

0.12

GERP RS

-0.52

Varity_R

0.10

gMVP

0.080

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over