CFAP52 p.Thr481Ser

Variant names:

• chr17-9635525-A-T
• NM_145054.5:c.1441A>T
• CFAP52 p.Thr481Ser

Your query was ambiguous. Multiple possible variants found:

• chr17-9635525-A-T
• chr17-9635526-C-G
• chr17-9635525-ACC-TCT
• chr17-9635525-ACC-TCA
• chr17-9635525-ACC-TCG
• chr17-9635526-CC-GT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_145054.5(CFAP52):​c.1441A>T​(p.Thr481Ser) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CFAP52 NM_145054.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760
• Publications: 0 publications found

Genes affected

CFAP52 (HGNC:16053): (cilia and flagella associated protein 52) WD repeat-containing proteins, such as WDR16, play crucial roles in a wide range of physiologic functions, including signal transduction, RNA processing, remodeling the cytoskeleton, regulation of vesicular traffic, and cell division (Silva et al., 2005 [PubMed 15967112]).[supplied by OMIM, Mar 2008]

CFAP52 Gene-Disease associations (from GenCC):

• situs inversus

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• visceral heterotaxy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.116102934).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145054.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP52	NM_145054.5	MANE Select	c.1441A>T	p.Thr481Ser	missense	Exon 11 of 14	NP_659491.4
	CFAP52	NM_001080556.2		c.1237A>T	p.Thr413Ser	missense	Exon 10 of 13	NP_001074025.1	Q8N1V2-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP52	ENST00000352665.10	TSL:1 MANE Select	c.1441A>T	p.Thr481Ser	missense	Exon 11 of 14	ENSP00000339449.5	Q8N1V2-1
	CFAP52	ENST00000396219.7	TSL:2	c.1237A>T	p.Thr413Ser	missense	Exon 10 of 13	ENSP00000379521.3	Q8N1V2-3
	CFAP52	ENST00000574097.1	TSL:3	c.94A>T	p.Thr32Ser	missense	Exon 1 of 3	ENSP00000468193.1	K7ERC0

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.80
DEOGEN2	Benign	0.017	T
Eigen	Benign	-0.83
Eigen_PC	Benign	-0.61
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.61	T
M_CAP	Benign	0.0060	T
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-0.99	T
PhyloP100		0.76
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	0.010	N
REVEL	Benign	0.074
Sift	Benign	1.0	T
Sift4G	Benign	0.91	T
PromoterAI		-0.020	Neutral
Varity_R		0.030
gMVP		0.13
Mutation Taster		=86/14	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-9538842;