NM_003059.3:c.225C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003059.3(SLC22A4):c.225C>T(p.Arg75Arg) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
SLC22A4
NM_003059.3 synonymous
NM_003059.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.263
Publications
0 publications found
Genes affected
SLC22A4 (HGNC:10968): (solute carrier family 22 member 4) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is an organic cation transporter and plasma integral membrane protein containing eleven putative transmembrane domains as well as a nucleotide-binding site motif. Transport by this protein is at least partially ATP-dependent. [provided by RefSeq, Jul 2008]
P4HA2 (HGNC:8547): (prolyl 4-hydroxylase subunit alpha 2) This gene encodes a component of prolyl 4-hydroxylase, a key enzyme in collagen synthesis composed of two identical alpha subunits and two beta subunits. The encoded protein is one of several different types of alpha subunits and provides the major part of the catalytic site of the active enzyme. In collagen and related proteins, prolyl 4-hydroxylase catalyzes the formation of 4-hydroxyproline that is essential to the proper three-dimensional folding of newly synthesized procollagen chains. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
P4HA2 Gene-Disease associations (from GenCC):
- myopiaInheritance: AD Classification: STRONG Submitted by: G2P
- myopia 25, autosomal dominantInheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 5-132294841-C-T is Benign according to our data. Variant chr5-132294841-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1370323.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.263 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A4 | NM_003059.3 | c.225C>T | p.Arg75Arg | synonymous_variant | Exon 1 of 10 | ENST00000200652.4 | NP_003050.2 | |
SLC22A4 | XM_047417594.1 | c.225C>T | p.Arg75Arg | synonymous_variant | Exon 1 of 8 | XP_047273550.1 | ||
SLC22A4 | XM_011543589.3 | c.225C>T | p.Arg75Arg | synonymous_variant | Exon 1 of 8 | XP_011541891.1 | ||
SLC22A4 | XM_006714675.5 | c.-200C>T | 5_prime_UTR_variant | Exon 1 of 9 | XP_006714738.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A4 | ENST00000200652.4 | c.225C>T | p.Arg75Arg | synonymous_variant | Exon 1 of 10 | 1 | NM_003059.3 | ENSP00000200652.3 | ||
P4HA2 | ENST00000471826.1 | n.138+337G>A | intron_variant | Intron 1 of 3 | 1 | |||||
P4HA2 | ENST00000431054.5 | c.78+337G>A | intron_variant | Intron 1 of 5 | 4 | ENSP00000391257.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 24, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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