ZSWIM5

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			154 clinvar	2 clinvar	1 clinvar	157
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	158	2	1	161

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020883.2	RefSeq	NP_065934.1	14	MANE Select
ENST00000359600.6	Ensembl	ENSP00000352614.5	14	MANE Select
ENST00000937275.1	Ensembl	ENSP00000607334.1	12	Standard
ENST00000937275.2	Ensembl	ENSP00000607334.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of axon guidance

Molecular Function

zinc ion binding

Cellular Component

extracellular space
Cul2-RING ubiquitin ligase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359600
Coding exons: 14
Length: 289811
Individuals with no LoFs: 124765
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 124798
p: 0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.32	471	635	0.741	0.0000348	7586
Missense (PolyPhen)		35	38.976	0.89799		425
Synonymous	2.68	199	253	0.786	0.0000127	2480
Loss of Function	5.10	14	54.8	0.256	0.00000322	565

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000098	0.000097	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.687
RVIS EVS: -0.73
RVIS percentile EVS: 14.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.131

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium