SEC23B

Chr 20ADAR

SEC23 homolog B, COPII component

Also known as: CDA-II, CDAII, CDAN2, CWS7, HEMPAS, hSec23B

NCBI Gene: 10483 ENSG00000101310 UniProt: Q15437 OMIM: 610512

SEC23B encodes a component of the COPII coat protein complex that promotes formation of transport vesicles from the endoplasmic reticulum and selects cargo molecules for transport to the Golgi complex. Mutations cause congenital dyserythropoietic anemia type II and possibly Cowden syndrome 7, with both autosomal dominant and autosomal recessive inheritance patterns reported. The gene shows low constraint against loss-of-function variants, suggesting tolerance to certain types of mutations.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a member of the SEC23 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec23p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The function of this gene product has been implicated in cargo selection and concentration. Multiple alternatively spliced transcript variants have been identified in this gene. [provided by RefSeq, Feb 2010]

GeneReviews OMIM ResearchGenerating clinical summary…

MultiplemechanismAD/ARLOEUF 0.982 OMIM phenotypes

Clinical Summary— SEC23B

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Gene-Disease Validity (ClinGen)

congenital dyserythropoietic anemia type 2 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

103 unique Pathogenic / Likely Pathogenic· 214 VUS of 828 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — SEC23B

Authoritative clinical overview · Recommended first read

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.98LOEUF

pLI 0.000

Z-score 1.68

OE 0.74 (0.57–0.98)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.47Z-score

OE missense 0.93 (0.86–1.02)

390 obs / 417.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.74 (0.57–0.98)

0≤0.351.4

Missense OE?0.93 (0.86–1.02)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 37 / 49.8Missense obs/exp: 390 / 417.2Syn Z: 0.29

ClinVar Variant Classifications

828 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic52

Likely Pathogenic51

VUS214

Likely Benign372

Benign67

Conflicting44

Pathogenic

Likely Pathogenic

214

VUS

372

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	43	3	6	0	52
Likely Pathogenic	38	12	1	0	51
VUS	2	184	26	2	214
Likely Benign	0	6	179	187	372
Benign	0	2	63	2	67
Conflicting	—				44
Total	83	207	275	191	800

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

26 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap SEC23B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →