rs1571096022

Variant names:

• chr1-167685436-C-A
• rs1571096022
• NM_052862.4:c.124C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-167685436-C-A
• chr1-167685436-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_052862.4(RCSD1):​c.124C>A​(p.Pro42Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P42S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RCSD1 NM_052862.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.01

Genes affected

RCSD1 (HGNC:28310): (RCSD domain containing 1) Enables actin filament binding activity. Involved in cellular hyperosmotic response. Predicted to be located in actin filament. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RCSD1	NM_052862.4	c.124C>A	p.Pro42Thr	missense_variant	Exon 3 of 7	ENST00000367854.8	NP_443094.3
RCSD1	NM_001322923.2	c.108+1435C>A		intron_variant	Intron 2 of 5		NP_001309852.1
RCSD1	NM_001322924.2	c.108+1435C>A		intron_variant	Intron 2 of 4		NP_001309853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RCSD1	ENST00000367854.8	c.124C>A	p.Pro42Thr	missense_variant	Exon 3 of 7	1	NM_052862.4	ENSP00000356828.3
RCSD1	ENST00000537350.5	c.108+1435C>A		intron_variant	Intron 2 of 5	1		ENSP00000439409.1
RCSD1	ENST00000361496.3	c.124C>A	p.Pro42Thr	missense_variant	Exon 3 of 5	3		ENSP00000355291.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.30	T;.
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.90	D;D
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.68	D;D
MetaSVM	Benign	-0.43	T
MutationAssessor	Uncertain	2.3	M;.
PrimateAI	Uncertain	0.53	T
PROVEAN	Uncertain	-4.3	D;D
REVEL	Uncertain	0.33
Sift	Uncertain	0.0030	D;D
Sift4G	Uncertain	0.010	D;D
Polyphen		1.0	D;.
Vest4		0.78
MutPred		0.43		Gain of phosphorylation at P42 (P = 0.0056);Gain of phosphorylation at P42 (P = 0.0056);
MVP		0.87
MPC		0.25
ClinPred		0.98	D
GERP RS		5.2
Varity_R		0.37
gMVP		0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571096022; hg19: chr1-167654673;